X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=8a6e8ae3bcc2619b7b24652f25b3b689213a9fd8;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=bb6f22384f7706861b1ed0b72cb2ad889ce4b183;hpb=cef7be0f9008ff15318e3479a5de35e127071ef3;p=jalview.git

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index bb6f223..8a6e8ae 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -20,12 +20,21 @@
  */
 package jalview.jbgui;
 
+import jalview.bin.Cache;
 import jalview.fts.core.FTSDataColumnPreferences;
 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
 import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.gui.Desktop;
+import jalview.gui.JalviewBooleanRadioButtons;
+import jalview.gui.JvOptionPane;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFilenameParts;
+import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
+import jalview.io.IntKeyStringValueEntry;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -40,28 +49,36 @@ import java.awt.Insets;
 import java.awt.Rectangle;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
 import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.Arrays;
+import java.util.List;
 
 import javax.swing.AbstractButton;
 import javax.swing.AbstractCellEditor;
 import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
 import javax.swing.ButtonGroup;
 import javax.swing.DefaultListCellRenderer;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
+import javax.swing.JComponent;
 import javax.swing.JFileChooser;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JRadioButton;
 import javax.swing.JScrollPane;
+import javax.swing.JSpinner;
 import javax.swing.JTabbedPane;
 import javax.swing.JTable;
+import javax.swing.JTextArea;
 import javax.swing.JTextField;
 import javax.swing.ListSelectionModel;
+import javax.swing.SpinnerModel;
+import javax.swing.SpinnerNumberModel;
 import javax.swing.SwingConstants;
 import javax.swing.border.Border;
 import javax.swing.border.EmptyBorder;
@@ -72,6 +89,8 @@ import javax.swing.event.ChangeListener;
 import javax.swing.table.TableCellEditor;
 import javax.swing.table.TableCellRenderer;
 
+import net.miginfocom.swing.MigLayout;
+
 /**
  * Base class for the Preferences panel.
  * 
@@ -85,6 +104,9 @@ public class GPreferences extends JPanel
   private static final Font LABEL_FONT_ITALIC = JvSwingUtils
           .getLabelFont(false, true);
 
+  private static final Font LABEL_FONT_BOLD = JvSwingUtils
+          .getLabelFont(true, false);
+
   /*
    * Visual tab components
    */
@@ -187,6 +209,19 @@ public class GPreferences extends JPanel
   protected JComboBox<String> nucColour = new JComboBox<>();
 
   /*
+   * Overview tab components
+   */
+  protected JPanel gapColour = new JPanel();
+
+  protected JPanel hiddenColour = new JPanel();
+
+  protected JCheckBox useLegacyGap;
+
+  protected JCheckBox showHiddenAtStart;
+
+  protected JLabel gapLabel;
+
+  /*
    * Connections tab components
    */
   protected JTable linkUrlTable = new JTable();
@@ -224,6 +259,10 @@ public class GPreferences extends JPanel
    */
   protected JComboBox<Object> epsRendering = new JComboBox<>();
 
+  protected JComboBox<Object> htmlRendering = new JComboBox<>();
+
+  protected JComboBox<Object> svgRendering = new JComboBox<>();
+
   protected JLabel userIdWidthlabel = new JLabel();
 
   protected JCheckBox autoIdWidth = new JCheckBox();
@@ -260,41 +299,70 @@ public class GPreferences extends JPanel
   /*
    * hmmer tab and components
    */
-  protected JPanel hmmerTab = new JPanel();
+  protected JPanel hmmerTab;
+
+  protected JCheckBox hmmrTrimTermini;
+
+  protected AbstractButton hmmerBackgroundUniprot;
+
+  protected AbstractButton hmmerBackgroundAlignment;
+
+  protected JTextField hmmerSequenceCount;
+
+  protected JTextField hmmerPath;
+
+  protected JTextField cygwinPath;
+
+  /*
+   * Web Services tab
+   */
+  protected JPanel wsTab = new JPanel();
+
+  /*
+   * Backups tab components
+   * a lot of these are member variables instead of local variables only so that they
+   * can be enabled/disabled easily in one go
+   */
 
-  protected JCheckBox trimTermini = new JCheckBox();
+  protected JCheckBox enableBackupFiles = new JCheckBox();
 
-  protected ButtonGroup backgroundFreqSource = new ButtonGroup();
+  protected JPanel presetsPanel = new JPanel();
 
-  protected AbstractButton uniprot = new JCheckBox();
+  protected JLabel presetsComboLabel = new JLabel();
 
-  protected AbstractButton alignment = new JCheckBox();
+  protected JCheckBox customiseCheckbox = new JCheckBox();
 
-  protected JLabel sequencesToKeep = new JLabel();
+  protected JButton revertButton = new JButton();
 
-  protected JTextField numberOfSequencesToKeepField = new JTextField();
+  protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
 
-  protected JLabel installationLocation = new JLabel();
+  private int backupfilesPresetsComboLastSelected = 0;
 
-  protected JCheckBox isHMMERInstalled = new JCheckBox();
+  protected JPanel suffixPanel = new JPanel();
 
-  protected JTextField hmmerPath = new JTextField();
+  protected JPanel keepfilesPanel = new JPanel();
 
-  protected JLabel hmmsearch = new JLabel();
+  protected JPanel exampleFilesPanel = new JPanel();
 
-  protected JLabel hmmalign = new JLabel();
+  protected JTextField suffixTemplate = new JTextField(null, 8);
 
-  /*
-   * DAS Settings tab
-   */
-  protected JPanel dasTab = new JPanel();
+  protected JLabel suffixTemplateLabel = new JLabel();
 
-  /*
-   * Web Services tab
-   */
-  protected JPanel wsTab = new JPanel();
+  protected JLabel suffixDigitsLabel = new JLabel();
+
+  protected JSpinner suffixDigitsSpinner = new JSpinner();
 
+  protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons();
 
+  protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons();
+
+  public JSpinner backupfilesRollMaxSpinner = new JSpinner();
+
+  protected JLabel oldBackupFilesLabel = new JLabel();
+
+  protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons();
+
+  protected JTextArea backupfilesExampleLabel = new JTextArea();
 
   /**
    * Creates a new GPreferences object.
@@ -329,12 +397,21 @@ public class GPreferences extends JPanel
     tabbedPane.add(initColoursTab(),
             MessageManager.getString("label.colours"));
 
+    tabbedPane.add(initOverviewTab(),
+            MessageManager.getString("label.overview"));
+
     tabbedPane.add(initStructureTab(),
             MessageManager.getString("label.structure"));
 
     tabbedPane.add(initConnectionsTab(),
             MessageManager.getString("label.connections"));
 
+	if (!Platform.isJS()) 
+	{
+	  tabbedPane.add(initBackupsTab(), 
+			MessageManager.getString("label.backups"));
+	}
+
     tabbedPane.add(initLinksTab(),
             MessageManager.getString("label.urllinks"));
 
@@ -347,20 +424,17 @@ public class GPreferences extends JPanel
     tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
 
     /*
-     * See DasSourceBrowser for the real work of configuring this tab.
-     */
-    dasTab.setLayout(new BorderLayout());
-    tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
-
-    /*
      * See WsPreferences for the real work of configuring this tab.
      */
-    wsTab.setLayout(new BorderLayout());
-    tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+    if (!Platform.isJS())
+    {
+      wsTab.setLayout(new BorderLayout());
+      tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+    }
 
     /*
      * Handler to validate a tab before leaving it - currently only for
-     * Structure.
+     * Structure
      */
     tabbedPane.addChangeListener(new ChangeListener()
     {
@@ -378,16 +452,6 @@ public class GPreferences extends JPanel
             return;
           }
         }
-        else if (lastTab == hmmerTab
-                && tabbedPane.getSelectedComponent() != hmmerTab
-                && isHMMERInstalled.isSelected())
-        {
-          if (!validateHMMER())
-          {
-            tabbedPane.setSelectedComponent(hmmerTab);
-          }
-          return;
-        }
         lastTab = tabbedPane.getSelectedComponent();
       }
 
@@ -424,51 +488,29 @@ public class GPreferences extends JPanel
   }
 
   /**
-   * Initialises the hmmer tabbed panel.
+   * Initialises the hmmer tabbed panel
    * 
    * @return
    */
   private JPanel initHMMERTab()
   {
-    hmmerTab.setLayout(null);
-
-    hmmalign.setFont(LABEL_FONT);
-    hmmalign.setText(MessageManager.getString("label.hmmalign_label"));
-    hmmalign.setBounds(new Rectangle(22, 10, 200, 23));
+    hmmerTab = new JPanel();
+    hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS));
+    hmmerTab.setLayout(new MigLayout("flowy"));
 
-    trimTermini.setFont(LABEL_FONT);
-    trimTermini.setText(MessageManager.getString("label.trim_termini"));
-    trimTermini.setBounds(new Rectangle(22, 30, 200, 23));
-
-    hmmsearch.setFont(LABEL_FONT);
-    hmmsearch.setText(MessageManager.getString("label.hmmsearch_label"));
-    hmmsearch.setBounds(new Rectangle(250, 10, 200, 23));
-
-    sequencesToKeep.setFont(LABEL_FONT);
-    sequencesToKeep
-            .setText(MessageManager.getString("label.no_of_sequences"));
-    sequencesToKeep.setBounds(new Rectangle(250, 30, 125, 23));
-    numberOfSequencesToKeepField.setBounds(new Rectangle(375, 30, 40, 23));
-
-    isHMMERInstalled.setFont(LABEL_FONT);
-    isHMMERInstalled.setText(
-            MessageManager.getString("label.hmmer_installed"));
-    isHMMERInstalled.setBounds(new Rectangle(22, 180, 200, 23));
-    isHMMERInstalled.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        boolean status = isHMMERInstalled.isSelected();
-        installationLocation.setEnabled(status);
-        hmmerPath.setEnabled(status);
-      }
-    });
-    installationLocation.setFont(LABEL_FONT);
-    installationLocation.setText(
-            MessageManager.getString("label.change_hmmer_location"));
-    installationLocation.setBounds(new Rectangle(22, 200, 200, 23));
-    hmmerPath.setBounds(new Rectangle(22, 220, 200, 23));
+    /*
+     * path to hmmer binaries folder
+     */
+    JPanel installationPanel = new JPanel(new MigLayout("flowy"));
+    // new FlowLayout(FlowLayout.LEFT));
+    JvSwingUtils.createTitledBorder(installationPanel,
+            MessageManager.getString("label.installation"), true);
+    hmmerTab.add(installationPanel);
+    JLabel hmmerLocation = new JLabel(
+            MessageManager.getString("label.hmmer_location"));
+    hmmerLocation.setFont(LABEL_FONT);
+    final int pathFieldLength = 40;
+    hmmerPath = new JTextField(pathFieldLength);
     hmmerPath.addMouseListener(new MouseAdapter()
     {
       @Override
@@ -480,34 +522,95 @@ public class GPreferences extends JPanel
           if (chosen != null)
           {
             hmmerPath.setText(chosen);
+            validateHmmerPath();
           }
         }
       }
     });
+    installationPanel.add(hmmerLocation);
+    installationPanel.add(hmmerPath);
+
+    /*
+     * path to Cygwin binaries folder (for Windows)
+     */
+    if (Platform.isWindowsAndNotJS())
+    {
+      JLabel cygwinLocation = new JLabel(
+              MessageManager.getString("label.cygwin_location"));
+      cygwinLocation.setFont(LABEL_FONT);
+      cygwinPath = new JTextField(pathFieldLength);
+      cygwinPath.addMouseListener(new MouseAdapter()
+      {
+        @Override
+        public void mouseClicked(MouseEvent e)
+        {
+          if (e.getClickCount() == 2)
+          {
+            String chosen = openFileChooser(true);
+            if (chosen != null)
+            {
+              cygwinPath.setText(chosen);
+              validateCygwinPath();
+            }
+          }
+        }
+      });
+      installationPanel.add(cygwinLocation);
+      installationPanel.add(cygwinPath);
+    }
 
-    backgroundFreqSource.add(uniprot);
-    backgroundFreqSource.add(alignment);
-    backgroundFreqSource.setSelected(uniprot.getModel(), true);
-
-    uniprot.setText(MessageManager.getString("label.freq_uniprot"));
-    uniprot.setFont(LABEL_FONT);
-    uniprot.setBounds(new Rectangle(22, 260, 255, 23));
-
-    alignment.setText(MessageManager.getString("label.freq_alignment"));
-    alignment.setFont(LABEL_FONT);
-    alignment.setBounds(new Rectangle(22, 280, 255, 23));
-
-    hmmerTab.add(uniprot);
-    hmmerTab.add(alignment);
-    hmmerTab.add(hmmalign);
-    hmmerTab.add(hmmsearch);
-    hmmerTab.add(installationLocation);
-    hmmerTab.add(hmmerPath);
-    hmmerTab.add(trimTermini);
-    hmmerTab.add(sequencesToKeep);
-    hmmerTab.add(sequencesToKeep);
-    hmmerTab.add(numberOfSequencesToKeepField);
-    hmmerTab.add(isHMMERInstalled);
+    /*
+     * preferences for hmmalign
+     */
+    JPanel alignOptionsPanel = new JPanel(new MigLayout());
+    // new FlowLayout(FlowLayout.LEFT));
+    JvSwingUtils.createTitledBorder(alignOptionsPanel,
+            MessageManager.getString("label.hmmalign_options"), true);
+    hmmerTab.add(alignOptionsPanel);
+    hmmrTrimTermini = new JCheckBox();
+    hmmrTrimTermini.setFont(LABEL_FONT);
+    hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
+    alignOptionsPanel.add(hmmrTrimTermini);
+
+    /*
+     * preferences for hmmsearch
+     */
+    JPanel searchOptions = new JPanel(new MigLayout());
+    // FlowLayout(FlowLayout.LEFT));
+    JvSwingUtils.createTitledBorder(searchOptions,
+            MessageManager.getString("label.hmmsearch_options"), true);
+    hmmerTab.add(searchOptions);
+    JLabel sequencesToKeep = new JLabel(
+            MessageManager.getString("label.no_of_sequences"));
+    sequencesToKeep.setFont(LABEL_FONT);
+    searchOptions.add(sequencesToKeep);
+    hmmerSequenceCount = new JTextField(5);
+    searchOptions.add(hmmerSequenceCount);
+
+    /*
+     * preferences for Information Content annotation
+     */
+    // JPanel dummy = new JPanel(new FlowLayout(FlowLayout.LEFT));
+    JPanel annotationOptions = new JPanel(new MigLayout("left"));
+    JvSwingUtils.createTitledBorder(annotationOptions,
+            MessageManager.getString("label.information_annotation"), true);
+    // dummy.add(annotationOptions);
+    hmmerTab.add(annotationOptions);
+    ButtonGroup backgroundOptions = new ButtonGroup();
+    hmmerBackgroundUniprot = new JRadioButton(
+            MessageManager.getString("label.freq_uniprot"));
+    hmmerBackgroundUniprot.setFont(LABEL_FONT);
+    hmmerBackgroundAlignment = new JRadioButton(
+            MessageManager.getString("label.freq_alignment"));
+    hmmerBackgroundAlignment.setFont(LABEL_FONT);
+    backgroundOptions.add(hmmerBackgroundUniprot);
+    backgroundOptions.add(hmmerBackgroundAlignment);
+    backgroundOptions.setSelected(hmmerBackgroundUniprot.getModel(), true);
+    // disable buttons for now as annotation only uses Uniprot background
+    hmmerBackgroundAlignment.setEnabled(false);
+    hmmerBackgroundUniprot.setEnabled(false);
+    annotationOptions.add(hmmerBackgroundUniprot, "wrap");
+    annotationOptions.add(hmmerBackgroundAlignment);
 
     return hmmerTab;
   }
@@ -521,18 +624,35 @@ public class GPreferences extends JPanel
   {
     JPanel outputTab = new JPanel();
     outputTab.setLayout(null);
-    JLabel epsLabel = new JLabel();
+
+    JLabel epsLabel = new JLabel(
+            MessageManager.formatMessage("label.rendering_style", "EPS"));
     epsLabel.setFont(LABEL_FONT);
     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
-    epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+    epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
     epsRendering.setFont(LABEL_FONT);
-    epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+    epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
+    JLabel htmlLabel = new JLabel(
+            MessageManager.formatMessage("label.rendering_style", "HTML"));
+    htmlLabel.setFont(LABEL_FONT);
+    htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
+    htmlRendering.setFont(LABEL_FONT);
+    htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
+    JLabel svgLabel = new JLabel(
+            MessageManager.formatMessage("label.rendering_style", "SVG"));
+    svgLabel.setFont(LABEL_FONT);
+    svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
+    svgRendering.setFont(LABEL_FONT);
+    svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
+
     JLabel jLabel1 = new JLabel();
     jLabel1.setFont(LABEL_FONT);
     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
     jLabel1.setText(MessageManager.getString("label.append_start_end"));
     jLabel1.setFont(LABEL_FONT);
+
     fastajv.setFont(LABEL_FONT);
     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
@@ -549,7 +669,7 @@ public class GPreferences extends JPanel
     TitledBorder titledBorder2 = new TitledBorder(
             MessageManager.getString("label.file_output"));
     jPanel11.setBorder(titledBorder2);
-    jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+    jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
     GridLayout gridLayout3 = new GridLayout();
     jPanel11.setLayout(gridLayout3);
     gridLayout3.setRows(8);
@@ -568,7 +688,7 @@ public class GPreferences extends JPanel
             MessageManager.getString("label.automatically_set_id_width"));
     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
             .getString("label.adjusts_width_generated_eps_png")));
-    autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
+    autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
     autoIdWidth.addActionListener(new ActionListener()
     {
 
@@ -586,10 +706,10 @@ public class GPreferences extends JPanel
     userIdWidthlabel.setToolTipText(
             JvSwingUtils.wrapTooltip(true, MessageManager.getString(
                     "label.manually_specify_width_left_column")));
-    userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
+    userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
     userIdWidth.setText("");
-    userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
+    userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
     userIdWidth.addActionListener(new ActionListener()
     {
 
@@ -602,10 +722,10 @@ public class GPreferences extends JPanel
     modellerOutput.setFont(LABEL_FONT);
     modellerOutput
             .setText(MessageManager.getString("label.use_modeller_output"));
-    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+    modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
     embbedBioJSON.setFont(LABEL_FONT);
     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
-    embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
+    embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
 
     jPanel11.add(jLabel1);
     jPanel11.add(blcjv);
@@ -619,9 +739,19 @@ public class GPreferences extends JPanel
     outputTab.add(userIdWidth);
     outputTab.add(userIdWidthlabel);
     outputTab.add(modellerOutput);
-    outputTab.add(embbedBioJSON);
-    outputTab.add(epsLabel);
-    outputTab.add(epsRendering);
+    if (!Platform.isJS())
+    {
+      /*
+       * JalviewJS doesn't support Lineart option or SVG output
+       */
+      outputTab.add(embbedBioJSON);
+      outputTab.add(epsLabel);
+      outputTab.add(epsRendering);
+      outputTab.add(htmlLabel);
+      outputTab.add(htmlRendering);
+      outputTab.add(svgLabel);
+      outputTab.add(svgRendering);
+    }
     outputTab.add(jPanel11);
     return outputTab;
   }
@@ -644,7 +774,9 @@ public class GPreferences extends JPanel
             MessageManager.getString("label.default_browser_unix"));
     defaultBrowser.setFont(LABEL_FONT);
     defaultBrowser.setText("");
-
+    final String tooltip = JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.double_click_to_browse"));
+    defaultBrowser.setToolTipText(tooltip);
     defaultBrowser.addMouseListener(new MouseAdapter()
     {
       @Override
@@ -691,6 +823,8 @@ public class GPreferences extends JPanel
                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
                     new Insets(0, 2, 5, 5), 70, 1));
 
+    versioncheck.setVisible(false);
+
     // Add padding so the panel doesn't look ridiculous
     JPanel spacePanel = new JPanel();
     connectTab.add(spacePanel,
@@ -712,6 +846,7 @@ public class GPreferences extends JPanel
     linkTab.setLayout(new GridBagLayout());
 
     // Set up table for Url links
+    linkUrlTable.getTableHeader().setReorderingAllowed(false);
     linkUrlTable.setFillsViewportHeight(true);
     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
     linkUrlTable.setAutoCreateRowSorter(true);
@@ -1065,7 +1200,7 @@ public class GPreferences extends JPanel
     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
     protColourLabel.setText(
             MessageManager.getString("label.prot_alignment_colour") + " ");
-    JvSwingUtils.addtoLayout(coloursTab,
+    GPreferences.addtoLayout(coloursTab,
             MessageManager
                     .getString("label.default_colour_scheme_for_alignment"),
             protColourLabel, protColour);
@@ -1077,7 +1212,7 @@ public class GPreferences extends JPanel
     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
     nucColourLabel.setText(
             MessageManager.getString("label.nuc_alignment_colour") + " ");
-    JvSwingUtils.addtoLayout(coloursTab,
+    GPreferences.addtoLayout(coloursTab,
             MessageManager
                     .getString("label.default_colour_scheme_for_alignment"),
             nucColourLabel, nucColour);
@@ -1086,11 +1221,11 @@ public class GPreferences extends JPanel
     annotationShding.setBorder(new TitledBorder(
             MessageManager.getString("label.annotation_shading_default")));
     annotationShding.setLayout(new GridLayout(1, 2));
-    JvSwingUtils.addtoLayout(annotationShding,
+    GPreferences.addtoLayout(annotationShding,
             MessageManager.getString(
                     "label.default_minimum_colour_annotation_shading"),
             mincolourLabel, minColour);
-    JvSwingUtils.addtoLayout(annotationShding,
+    GPreferences.addtoLayout(annotationShding,
             MessageManager.getString(
                     "label.default_maximum_colour_annotation_shading"),
             maxcolourLabel, maxColour);
@@ -1099,6 +1234,150 @@ public class GPreferences extends JPanel
   }
 
   /**
+   * Initialises the Overview tabbed panel.
+   * 
+   * @return
+   */
+  private JPanel initOverviewTab()
+  {
+    JPanel overviewPanel = new JPanel();
+    overviewPanel.setBorder(new TitledBorder(
+            MessageManager.getString("label.overview_settings")));
+
+    gapColour.setFont(LABEL_FONT);
+    // fixing the border colours stops apparent colour bleed from the panel
+    gapColour.setBorder(
+            BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
+    gapColour.setPreferredSize(new Dimension(40, 20));
+    gapColour.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        gapColour_actionPerformed(gapColour);
+      }
+    });
+
+    hiddenColour.setFont(LABEL_FONT);
+    // fixing the border colours stops apparent colour bleed from the panel
+    hiddenColour.setBorder(
+            BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
+    hiddenColour.setPreferredSize(new Dimension(40, 20));
+    hiddenColour.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        hiddenColour_actionPerformed(hiddenColour);
+      }
+    });
+
+    useLegacyGap = new JCheckBox(
+            MessageManager.getString("label.ov_legacy_gap"));
+    useLegacyGap.setFont(LABEL_FONT);
+    useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
+    useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
+    gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
+    gapLabel.setFont(LABEL_FONT);
+    gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    gapLabel.setVerticalTextPosition(SwingConstants.TOP);
+    showHiddenAtStart = new JCheckBox(
+            MessageManager.getString("label.ov_show_hide_default"));
+    showHiddenAtStart.setFont(LABEL_FONT);
+    showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
+    showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
+    JLabel hiddenLabel = new JLabel(
+            MessageManager.getString("label.hidden_colour"));
+    hiddenLabel.setFont(LABEL_FONT);
+    hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
+
+    useLegacyGap.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        useLegacyGaps_actionPerformed(e);
+      }
+    });
+
+    overviewPanel.setLayout(new GridBagLayout());
+    GridBagConstraints c1 = new GridBagConstraints();
+
+    c1.fill = GridBagConstraints.HORIZONTAL;
+    c1.gridx = 0;
+    c1.gridy = 0;
+    c1.weightx = 1;
+    c1.ipady = 20;
+    c1.anchor = GridBagConstraints.FIRST_LINE_START;
+    overviewPanel.add(useLegacyGap, c1);
+
+    GridBagConstraints c2 = new GridBagConstraints();
+    c2.fill = GridBagConstraints.HORIZONTAL;
+    c2.gridx = 1;
+    c2.gridy = 0;
+    c2.insets = new Insets(0, 15, 0, 10);
+    overviewPanel.add(gapLabel, c2);
+
+    GridBagConstraints c3 = new GridBagConstraints();
+    c3.fill = GridBagConstraints.HORIZONTAL;
+    c3.gridx = 2;
+    c3.gridy = 0;
+    c3.insets = new Insets(0, 0, 0, 15);
+    overviewPanel.add(gapColour, c3);
+
+    GridBagConstraints c4 = new GridBagConstraints();
+    c4.fill = GridBagConstraints.HORIZONTAL;
+    c4.gridx = 0;
+    c4.gridy = 1;
+    c4.weightx = 1;
+    overviewPanel.add(showHiddenAtStart, c4);
+
+    GridBagConstraints c5 = new GridBagConstraints();
+    c5.fill = GridBagConstraints.HORIZONTAL;
+    c5.gridx = 1;
+    c5.gridy = 1;
+    c5.insets = new Insets(0, 15, 0, 10);
+    overviewPanel.add(hiddenLabel, c5);
+
+    GridBagConstraints c6 = new GridBagConstraints();
+    c6.fill = GridBagConstraints.HORIZONTAL;
+    c6.gridx = 2;
+    c6.gridy = 1;
+    c6.insets = new Insets(0, 0, 0, 15);
+    overviewPanel.add(hiddenColour, c6);
+
+    JButton resetButton = new JButton(
+            MessageManager.getString("label.reset_to_defaults"));
+
+    resetButton.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        resetOvDefaults_actionPerformed(e);
+      }
+    });
+
+    GridBagConstraints c7 = new GridBagConstraints();
+    c7.fill = GridBagConstraints.NONE;
+    c7.gridx = 0;
+    c7.gridy = 2;
+    c7.insets = new Insets(10, 0, 0, 0);
+    c7.anchor = GridBagConstraints.WEST;
+    overviewPanel.add(resetButton, c7);
+
+    // Add padding so the panel doesn't look ridiculous
+    JPanel spacePanel = new JPanel();
+    overviewPanel.add(spacePanel,
+            new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
+                    GridBagConstraints.WEST, GridBagConstraints.BOTH,
+                    new Insets(0, 0, 0, 5), 0, 0));
+
+    return overviewPanel;
+  }
+
+  /**
    * Initialises the Structure tabbed panel.
    * 
    * @return
@@ -1181,14 +1460,14 @@ public class GPreferences extends JPanel
     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
     pathLabel.setText(MessageManager.getString("label.chimera_path"));
-    final String tooltip = JvSwingUtils.wrapTooltip(true,
-            MessageManager.getString("label.chimera_path_tip"));
-    pathLabel.setToolTipText(tooltip);
     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
     structureTab.add(pathLabel);
 
     chimeraPath.setFont(LABEL_FONT);
     chimeraPath.setText("");
+    final String tooltip = JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.chimera_path_tip"));
+    chimeraPath.setToolTipText(tooltip);
     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
     chimeraPath.addMouseListener(new MouseAdapter()
     {
@@ -1234,6 +1513,17 @@ public class GPreferences extends JPanel
     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
     structureTab.add(docFieldPref);
 
+    /*
+     * hide Chimera options in JalviewJS
+     */
+    if (Platform.isJS()) 
+    {
+      pathLabel.setVisible(false);
+      chimeraPath.setVisible(false);
+      viewerLabel.setVisible(false);
+      structViewer.setVisible(false);
+    }
+    
     return structureTab;
   }
 
@@ -1275,46 +1565,11 @@ public class GPreferences extends JPanel
     return choice;
   }
 
-  /**
-   * Validate the structure tab preferences; if invalid, set focus on this tab.
-   * 
-   * @param e
-   */
-  protected boolean validateStructure(FocusEvent e)
-  {
-    if (!validateStructure())
-    {
-      e.getComponent().requestFocusInWindow();
-      return false;
-    }
-    return true;
-  }
-
-  /**
-   * Validate the hmmer tab preferences; if invalid, set focus on this tab.
-   * 
-   * @param e
-   */
-  protected boolean validateHMMER(FocusEvent e)
-  {
-    if (!validateHMMER())
-    {
-      e.getComponent().requestFocusInWindow();
-      return false;
-    }
-    return true;
-  }
-
   protected boolean validateStructure()
   {
     return false;
   }
 
-  protected boolean validateHMMER()
-  {
-    return false;
-  }
-
   /**
    * Initialises the Visual tabbed panel.
    * 
@@ -1511,6 +1766,9 @@ public class GPreferences extends JPanel
     startupCheckbox.setSelected(true);
     startupFileTextfield.setFont(LABEL_FONT);
     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
+    final String tooltip = JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.double_click_to_browse"));
+    startupFileTextfield.setToolTipText(tooltip);
     startupFileTextfield.addMouseListener(new MouseAdapter()
     {
       @Override
@@ -1631,115 +1889,1092 @@ public class GPreferences extends JPanel
     visualTab.add(fontNameCB);
     visualTab.add(fontSizeCB);
     visualTab.add(fontStyleCB);
+    
+    if (Platform.isJS())
+    {
+      startupCheckbox.setVisible(false);
+      startupFileTextfield.setVisible(false);
+    }
+    
     return visualTab;
   }
 
-  protected void autoIdWidth_actionPerformed()
-  {
-    // TODO Auto-generated method stub
-
-  }
+  /**
+   * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
+   */
 
-  protected void userIdWidth_actionPerformed()
+  protected void loadLastSavedBackupsOptions()
   {
-    // TODO Auto-generated method stub
+    BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
+            .getSavedBackupEntry();
+    enableBackupFiles
+            .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
+
+    BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
+            .createBackupFilesPresetEntry(Cache
+                    .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
+    if (backupfilesCustomEntry == null)
+    {
+      backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+              .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
+    }
+    BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+            BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
+            backupfilesCustomEntry);
 
-  }
+    setComboIntStringKey(backupfilesPresetsCombo,
+            Cache.getDefault(BackupFiles.NS + "_PRESET",
+                    BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
 
-  protected void maxColour_actionPerformed(JPanel panel)
-  {
-  }
+    backupsSetOptions(savedPreset);
 
-  protected void minColour_actionPerformed(JPanel panel)
-  {
+    backupsOptionsSetEnabled();
+    updateBackupFilesExampleLabel();
   }
 
-  protected void showunconserved_actionPerformed(ActionEvent e)
+  private boolean warnAboutSuffixReverseChange()
   {
-    // TODO Auto-generated method stub
-
+    BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+            .getSavedBackupEntry();
+    boolean savedSuffixReverse = bfpe.reverse;
+    int savedSuffixDigits = bfpe.digits;
+    String savedSuffixTemplate = bfpe.suffix;
+
+    boolean nowSuffixReverse = suffixReverse.isSelected();
+    int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
+    String nowSuffixTemplate = suffixTemplate.getText();
+    return nowSuffixReverse != savedSuffixReverse
+            && nowSuffixDigits == savedSuffixDigits
+            && nowSuffixTemplate != null
+            && nowSuffixTemplate.equals(savedSuffixTemplate);
   }
 
   /**
-   * DOCUMENT ME!
+   * Initialises the Backups tabbed panel.
    * 
-   * @param e
-   *          DOCUMENT ME!
+   * @return
    */
-  public void ok_actionPerformed(ActionEvent e)
+  private JPanel initBackupsTab()
   {
-  }
+    JPanel backupsTab = new JPanel();
+    backupsTab.setBorder(new TitledBorder(
+            MessageManager.getString("label.backup_files")));
+    backupsTab.setLayout(new GridBagLayout());
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-  }
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.weightx = 0.0;
+    gbc.weighty = 0.0;
+    gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+    gbc.fill = GridBagConstraints.NONE;
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-  }
+    initBackupsTabPresetsPanel();
+    initBackupsTabSuffixPanel();
+    initBackupsTabKeepFilesPanel();
+    initBackupsTabFilenameExamplesPanel();
 
-  /**
-   * DOCUMENT ME!
-   */
-  public void startupFileTextfield_mouseClicked()
-  {
-  }
+    enableBackupFiles.setFont(LABEL_FONT_BOLD);
+    enableBackupFiles
+            .setText(MessageManager.getString("label.enable_backupfiles"));
+    enableBackupFiles.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        // enable other options only when the first is checked
+        backupsOptionsSetEnabled();
+      }
+    });
 
-  public void newLink_actionPerformed(ActionEvent e)
-  {
 
-  }
+    // enable checkbox 1 col
+    gbc.gridwidth = 1;
+    gbc.gridheight = 1;
+    gbc.gridx = 0;
+    gbc.gridy = 0; // row 0
+    backupsTab.add(enableBackupFiles, gbc);
+
+    // summary of scheme box (over two rows)
+    gbc.gridx = 1;
+    gbc.weightx = 0.0;
+    gbc.gridheight = 2;
+    gbc.anchor = GridBagConstraints.FIRST_LINE_END;
+    gbc.fill = GridBagConstraints.BOTH;
+    backupsTab.add(exampleFilesPanel, gbc);
+    gbc.gridheight = 1;
+    gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+    gbc.fill = GridBagConstraints.NONE;
 
-  public void editLink_actionPerformed(ActionEvent e)
-  {
+    // fill empty space on right
+    gbc.gridx++;
+    gbc.weightx = 1.0;
+    backupsTab.add(new JPanel(), gbc);
 
-  }
+    // schemes box
+    gbc.weightx = 0.0;
+    gbc.gridx = 0;
+    gbc.gridy++; // row 1
+    backupsTab.add(presetsPanel, gbc);
 
-  public void deleteLink_actionPerformed(ActionEvent e)
-  {
+    // now using whole row
+    gbc.gridwidth = 2;
+    gbc.gridheight = 1;
+    // keep files box
+    gbc.gridx = 0;
+    gbc.gridy++; // row 2
+    backupsTab.add(keepfilesPanel, gbc);
 
-  }
+    // filename strategy box
+    gbc.gridy++; // row 3
+    backupsTab.add(suffixPanel, gbc);
 
-  public void defaultBrowser_mouseClicked(MouseEvent e)
-  {
+    // fill empty space
+    gbc.gridy++; // row 4
+    gbc.weighty = 1.0;
+    backupsTab.add(new JPanel(), gbc);
 
+    backupsOptionsSetEnabled();
+    return backupsTab;
   }
 
-  public void linkURLList_keyTyped(KeyEvent e)
+  private JPanel initBackupsTabPresetsPanel()
   {
 
-  }
+    String title = MessageManager.getString("label.schemes");
 
-  public void useProxy_actionPerformed()
-  {
-    boolean enabled = useProxy.isSelected();
-    portLabel.setEnabled(enabled);
-    serverLabel.setEnabled(enabled);
-    proxyServerTB.setEnabled(enabled);
-    proxyPortTB.setEnabled(enabled);
-  }
+    presetsPanel.setLayout(new GridBagLayout());
 
-  /**
-   * Customer renderer for JTable: supports column of radio buttons
-   */
-  public class RadioButtonRenderer extends JRadioButton
-          implements TableCellRenderer
-  {
-    public RadioButtonRenderer()
-    {
-      setHorizontalAlignment(CENTER);
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.weightx = 0.0;
+    gbc.weighty = 0.0;
+    gbc.anchor = GridBagConstraints.BASELINE_LEADING;
+    gbc.fill = GridBagConstraints.NONE;
+    gbc.gridwidth = 1;
+    gbc.gridheight = 1;
+
+    // "Scheme: "
+    gbc.gridx = 0;
+    gbc.gridy = 0;
+
+    presetsComboLabel = new JLabel(title + ":");
+    presetsPanel.add(presetsComboLabel, gbc);
+
+    List<Object> entries = Arrays
+            .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
+    List<String> tooltips = Arrays.asList(
+            BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
+    backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
+            tooltips);
+    /*
+    for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
+    {
+      backupfilesPresetsCombo
+              .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
+    }
+    */
+
+    backupfilesPresetsCombo.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        int key = getComboIntStringKey(backupfilesPresetsCombo);
+        if (!customiseCheckbox.isSelected())
+        {
+          backupfilesPresetsComboLastSelected = key;
+        }
+        if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+        {
+          if (customiseCheckbox.isSelected())
+          {
+            // got here by clicking on customiseCheckbox so don't change the values
+            backupfilesCustomOptionsSetEnabled();
+          }
+          else
+          {
+            backupsTabUpdatePresets();
+            backupfilesCustomOptionsSetEnabled();
+          }
+        }
+        else
+        {
+          customiseCheckbox.setSelected(false);
+          backupsTabUpdatePresets();
+          backupfilesCustomOptionsSetEnabled();
+        }
+      }
+    });
+
+    // dropdown list of preset schemes
+    gbc.gridx = 1;
+    presetsPanel.add(backupfilesPresetsCombo, gbc);
+
+    revertButton.setText(MessageManager.getString("label.cancel_changes"));
+    revertButton.setToolTipText(
+            MessageManager.getString("label.cancel_changes_description"));
+    revertButton.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        backupsSetOptions(
+                BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
+                        BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
+        backupfilesCustomOptionsSetEnabled();
+      }
+
+    });
+    revertButton.setFont(LABEL_FONT);
+
+    customiseCheckbox.setFont(LABEL_FONT);
+    customiseCheckbox.setText(MessageManager.getString("label.customise"));
+    customiseCheckbox.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        int currently = getComboIntStringKey(backupfilesPresetsCombo);
+        if (customiseCheckbox.isSelected())
+        {
+          backupfilesPresetsComboLastSelected = currently;
+          setComboIntStringKey(backupfilesPresetsCombo,
+                  BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+        }
+        else
+        {
+          setComboIntStringKey(backupfilesPresetsCombo,
+                  backupfilesPresetsComboLastSelected);
+
+        }
+        backupfilesCustomOptionsSetEnabled();
+      }
+    });
+    customiseCheckbox.setToolTipText(
+            MessageManager.getString("label.customise_description"));
+
+    // customise checkbox
+    gbc.gridx = 0;
+    gbc.gridy++;
+    presetsPanel.add(customiseCheckbox, gbc);
+
+    // "Cancel changes" button (aligned with combo box above)
+    gbc.gridx = 1;
+    presetsPanel.add(revertButton, gbc);
+
+    return presetsPanel;
+  }
+
+  private JPanel initBackupsTabFilenameExamplesPanel()
+  {
+    String title = MessageManager
+            .getString("label.scheme_examples");
+    TitledBorder tb = new TitledBorder(title);
+    exampleFilesPanel.setBorder(tb);
+    exampleFilesPanel.setLayout(new GridBagLayout());
+
+
+    backupfilesExampleLabel.setEditable(false);
+    backupfilesExampleLabel
+            .setBackground(exampleFilesPanel.getBackground());
+
+    updateBackupFilesExampleLabel();
+
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.weightx = 1.0;
+    gbc.weighty = 1.0;
+    gbc.fill = GridBagConstraints.NONE;
+    gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+
+    exampleFilesPanel.add(backupfilesExampleLabel, gbc);
+    return exampleFilesPanel;
+  }
+
+  private void backupsTabUpdatePresets()
+  {
+    IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
+            .getSelectedItem();
+    int key = entry.k;
+    String value = entry.v;
+
+    if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
+            .containsKey(key))
+    {
+      backupsSetOptions(
+              BackupFilesPresetEntry.backupfilesPresetEntriesValues
+                      .get(key));
+    }
+    else
+    {
+      Cache.log.error(
+              "Preset '" + value + "' [key:" + key + "] not implemented");
+    }
+
+    // Custom options will now be enabled when the customiseCheckbox is checked
+    // (performed above)
+    // backupfilesCustomOptionsSetEnabled();
+    updateBackupFilesExampleLabel();
+  }
+
+  protected int getComboIntStringKey(
+          JComboBox<Object> backupfilesPresetsCombo2)
+  {
+    IntKeyStringValueEntry e;
+    try
+    {
+      e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
+              .getSelectedItem();
+    } catch (Exception ex)
+    {
+      Cache.log.error(
+              "Problem casting Combo entry to IntKeyStringValueEntry.");
+      e = null;
+    }
+    return e != null ? e.k : 0;
+  }
+
+  protected void setComboIntStringKey(
+          JComboBox<Object> backupfilesPresetsCombo2,
+          int key)
+  {
+    for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
+    {
+      IntKeyStringValueEntry e;
+      try
+      {
+        e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
+      } catch (Exception ex)
+      {
+        Cache.log.error(
+                "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
+        continue;
+      }
+      if (e.k == key)
+      {
+        backupfilesPresetsCombo2.setSelectedIndex(i);
+        break;
+      }
+    }
+    // backupsTabUpdatePresets();
+  }
+
+  private JPanel initBackupsTabSuffixPanel()
+  {
+    suffixPanel.setBorder(new TitledBorder(
+            MessageManager.getString("label.backup_filename_strategy")));
+    suffixPanel.setLayout(new GridBagLayout());
+
+    suffixTemplateLabel
+            .setText(MessageManager.getString("label.append_to_filename"));
+    suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    suffixTemplateLabel.setFont(LABEL_FONT);
+
+    final String tooltip = JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.append_to_filename_tooltip"));
+    suffixTemplate.setToolTipText(tooltip);
+    suffixTemplate.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        updateBackupFilesExampleLabel();
+        backupfilesCustomOptionsSetEnabled();
+        backupfilesRevertButtonSetEnabled(true);
+      }
+
+    });
+    suffixTemplate.addKeyListener(new KeyListener()
+    {
+      @Override
+      public void keyReleased(KeyEvent e)
+      {
+        updateBackupFilesExampleLabel();
+        backupfilesCustomOptionsSetEnabled();
+        backupfilesRevertButtonSetEnabled(true);
+      }
+
+      @Override
+      public void keyPressed(KeyEvent e)
+      {
+      }
+
+      // disable use of ':' or '/' or '\'
+      @Override
+      public void keyTyped(KeyEvent e)
+      {
+        char c = e.getKeyChar();
+        if (c == ':' || c == '/' || c == '\\')
+        {
+          // don't process ':' or '/' or '\'
+          e.consume();
+        }
+      }
+
+    });
+
+    // digits spinner
+    suffixDigitsLabel
+            .setText(MessageManager.getString("label.index_digits"));
+    suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    suffixDigitsLabel.setFont(LABEL_FONT);
+    ChangeListener c = new ChangeListener()
+    {
+      @Override
+      public void stateChanged(ChangeEvent e)
+      {
+        backupfilesRevertButtonSetEnabled(true);
+        updateBackupFilesExampleLabel();
+      }
+
+    };
+    setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
+            BackupFilesPresetEntry.DIGITSMAX, 3, c);
+
+    suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
+            MessageManager.getString("label.increment_index"));
+    suffixReverse.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        boolean okay = true;
+        if (warnAboutSuffixReverseChange())
+        {
+          // Warning popup
+          okay = confirmSuffixReverseChange();
+        }
+        if (okay)
+        {
+          backupfilesRevertButtonSetEnabled(true);
+          updateBackupFilesExampleLabel();
+        }
+        else
+        {
+          boolean savedSuffixReverse = BackupFilesPresetEntry
+                  .getSavedBackupEntry().reverse;
+          suffixReverse.setSelected(savedSuffixReverse);
+        }
+      }
+    });
+
+    GridBagConstraints sgbc = new GridBagConstraints();
+
+    // first row (template text box)
+    sgbc.anchor = GridBagConstraints.WEST;
+    sgbc.gridx = 0;
+    sgbc.gridy = 0;
+    sgbc.gridwidth = 1;
+    sgbc.gridheight = 1;
+    sgbc.weightx = 1.0;
+    sgbc.weighty = 0.0;
+    sgbc.fill = GridBagConstraints.NONE;
+    suffixPanel.add(suffixTemplateLabel, sgbc);
+
+    sgbc.gridx = 1;
+    sgbc.fill = GridBagConstraints.HORIZONTAL;
+    suffixPanel.add(suffixTemplate, sgbc);
+
+    // second row (number of digits spinner)
+    sgbc.gridy = 1;
+
+    sgbc.gridx = 0;
+    sgbc.fill = GridBagConstraints.NONE;
+    suffixPanel.add(suffixDigitsLabel, sgbc);
+
+    sgbc.gridx = 1;
+    sgbc.fill = GridBagConstraints.HORIZONTAL;
+    suffixPanel.add(suffixDigitsSpinner, sgbc);
+
+    // third row (forward order radio selection)
+    sgbc.gridx = 0;
+    sgbc.gridy = 2;
+    sgbc.gridwidth = GridBagConstraints.REMAINDER;
+    sgbc.fill = GridBagConstraints.HORIZONTAL;
+    suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
+
+    // fourth row (reverse order radio selection)
+    sgbc.gridy = 3;
+    suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
+    return suffixPanel;
+  }
+
+  private boolean confirmSuffixReverseChange()
+  {
+    boolean ret = false;
+    String warningMessage = MessageManager
+            .getString("label.warning_confirm_change_reverse");
+    int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
+            warningMessage,
+            MessageManager.getString("label.change_increment_decrement"),
+            JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+
+    ret = (confirm == JvOptionPane.YES_OPTION);
+    return ret;
+  }
+
+  private JPanel initBackupsTabKeepFilesPanel()
+  {
+    keepfilesPanel.setBorder(
+            new TitledBorder(MessageManager.getString("label.keep_files")));
+    keepfilesPanel.setLayout(new GridBagLayout());
+
+    backupfilesKeepAll.setLabels(
+            MessageManager.getString("label.keep_all_backup_files"),
+            MessageManager.getString(
+                    "label.keep_only_this_number_of_backup_files"));
+    backupfilesKeepAll.addTrueActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        backupfilesRevertButtonSetEnabled(true);
+        updateBackupFilesExampleLabel();
+      }
+    });
+    backupfilesKeepAll.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        backupfilesRevertButtonSetEnabled(true);
+        keepRollMaxOptionsEnabled();
+        updateBackupFilesExampleLabel();
+      }
+    });
+
+    ChangeListener c = new ChangeListener()
+    {
+      @Override
+      public void stateChanged(ChangeEvent e)
+      {
+        backupfilesRevertButtonSetEnabled(true);
+        updateBackupFilesExampleLabel();
+      }
+
+    };
+    setIntegerSpinner(backupfilesRollMaxSpinner,
+            BackupFilesPresetEntry.ROLLMAXMIN,
+            BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
+
+    backupfilesConfirmDelete.setLabels(
+            MessageManager.getString("label.always_ask"),
+            MessageManager.getString("label.auto_delete"));
+    backupfilesConfirmDelete.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        backupfilesRevertButtonSetEnabled(true);
+      }
+    });
+    // update the enabled section
+    keepRollMaxOptionsEnabled();
+
+    GridBagConstraints kgbc = new GridBagConstraints();
+
+    // first row (template text box)
+    kgbc.anchor = GridBagConstraints.WEST;
+    kgbc.gridx = 0;
+    kgbc.gridy = 0;
+    kgbc.gridwidth = GridBagConstraints.REMAINDER;
+    kgbc.gridheight = 1;
+    kgbc.weightx = 1.0;
+    kgbc.weighty = 0.0;
+    kgbc.fill = GridBagConstraints.HORIZONTAL;
+    keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
+
+    // second row
+    kgbc.gridy = 1;
+
+    kgbc.gridx = 0;
+    kgbc.gridwidth = GridBagConstraints.RELATIVE;
+    keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
+
+    kgbc.gridx = 1;
+    kgbc.gridwidth = GridBagConstraints.REMAINDER;
+    keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
+
+    // third row (indented)
+    kgbc.gridy = 2;
+    kgbc.insets = new Insets(0, 20, 0, 0);
+
+    kgbc.gridx = 0;
+    kgbc.gridwidth = GridBagConstraints.REMAINDER;
+    kgbc.fill = GridBagConstraints.HORIZONTAL;
+    kgbc.weightx = 1.0;
+
+    JPanel jp = new JPanel();
+    jp.setLayout(new FlowLayout());
+    oldBackupFilesLabel
+            .setText(MessageManager
+                    .getString("label.autodelete_old_backup_files"));
+    oldBackupFilesLabel.setFont(LABEL_FONT);
+    oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    jp.add(oldBackupFilesLabel);
+    jp.add(backupfilesConfirmDelete.getTrueButton());
+    jp.add(backupfilesConfirmDelete.getFalseButton());
+    keepfilesPanel.add(jp, kgbc);
+
+    return keepfilesPanel;
+  }
+
+  protected void updateBackupFilesExampleLabel()
+  {
+    int exampleindex = 12;
+    String base = MessageManager.getString("label.filename") + ".fa";
+    if (base == null || base.length() == 0)
+    {
+      base = "file_name.fa";
+    }
+
+    boolean reverse = suffixReverse.isSelected();
+    boolean keepAll = backupfilesKeepAll.isSelected();
+    int rollMax = 4;
+    String suffix = suffixTemplate.getText();
+    int digits = 3;
+
+    backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
+    if (suffix == null || suffix.length() == 0)
+    {
+      backupfilesExampleLabel
+              .setText(MessageManager.getString("label.no_backup_files"));
+      backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
+      return;
+    }
+
+    rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
+    rollMax = rollMax < 1 ? 1 : rollMax;
+
+    if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
+    {
+      rollMax = 1;
+    }
+
+    digits = getSpinnerInt(suffixDigitsSpinner, 3);
+    digits = digits < 1 ? 1 : digits;
+
+    int lowersurround = 2;
+    int uppersurround = 0;
+    StringBuilder exampleSB = new StringBuilder();
+    boolean firstLine = true;
+    int lineNumber = 0;
+    if (reverse)
+    {
+
+      int min = 1;
+      int max = keepAll ? exampleindex : rollMax;
+      for (int index = min; index <= max; index++)
+      {
+        if (index == min + lowersurround && index < max - uppersurround - 1)
+        {
+          exampleSB.append("\n...");
+          lineNumber++;
+        }
+        else if (index > min + lowersurround && index < max - uppersurround)
+        {
+          // nothing
+        }
+        else
+        {
+          if (firstLine)
+          {
+            firstLine = false;
+          }
+          else
+          {
+            exampleSB.append("\n");
+            lineNumber++;
+          }
+          exampleSB.append(BackupFilenameParts.getBackupFilename(index,
+                  base, suffix, digits));
+          if (min == max)
+          {
+            // no extra text needed
+          }
+          else if (index == min)
+          {
+            String newest = MessageManager.getString("label.braced_newest");
+            if (newest != null && newest.length() > 0)
+            {
+              exampleSB.append(" " + newest);
+            }
+          }
+          else if (index == max)
+          {
+            String oldest = MessageManager.getString("label.braced_oldest");
+            if (oldest != null && oldest.length() > 0)
+            {
+              exampleSB.append(" " + oldest);
+            }
+          }
+        }
+      }
+    }
+    else
+    {
+
+      int min = (keepAll || exampleindex - rollMax < 0) ? 1
+              : exampleindex - rollMax + 1;
+      int max = exampleindex;
+
+      for (int index = min; index <= max; index++)
+      {
+
+        if (index == min + lowersurround && index < max - uppersurround - 1)
+        {
+          exampleSB.append("\n...");
+          lineNumber++;
+        }
+        else if (index > min + lowersurround && index < max - uppersurround)
+        {
+          // nothing
+        }
+        else
+        {
+          if (firstLine)
+          {
+            firstLine = false;
+          }
+          else
+          {
+            exampleSB.append("\n");
+            lineNumber++;
+          }
+          exampleSB.append(BackupFilenameParts.getBackupFilename(index,
+                  base, suffix, digits));
+          if (min == max)
+          {
+            // no extra text needed
+          }
+          else if (index == min)
+          {
+            String oldest = MessageManager.getString("label.braced_oldest");
+            if (oldest != null && oldest.length() > 0)
+            {
+              exampleSB.append(" " + oldest);
+            }
+          }
+          else if (index == max)
+          {
+            String newest = MessageManager.getString("label.braced_newest");
+            if (newest != null && newest.length() > 0)
+            {
+              exampleSB.append(" " + newest);
+            }
+          }
+        }
+      }
+
+    }
+
+    // add some extra empty lines to pad out the example files box. ugh, please tell
+    // me how to do this better
+    int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
+    if (remainingLines > 0)
+    {
+      for (int i = 0; i < remainingLines; i++)
+      {
+        exampleSB.append("\n ");
+        lineNumber++;
+      }
+    }
+
+    backupfilesExampleLabel.setText(exampleSB.toString());
+  }
+
+  protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
+          boolean useExistingVal, ChangeListener c)
+  {
+    int i = def;
+    if (useExistingVal)
+    {
+      try
+      {
+        i = ((Integer) s.getValue()).intValue();
+      } catch (Exception e)
+      {
+        Cache.log.error(
+                "Exception casting the initial value of s.getValue()");
+      }
+    }
+
+    setIntegerSpinner(s, min, max, i, c);
+  }
+
+  protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
+          ChangeListener c)
+  {
+    // integer spinner for number of digits
+    if (def > max)
+    {
+      max = def;
+    }
+    if (def < min)
+    {
+      def = min;
+    }
+    SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
+    s.setModel(sModel);
+
+    s.addChangeListener(c);
+
+  }
+
+  protected static int getSpinnerInt(JSpinner s, int def)
+  {
+    int i = def;
+    try
+    {
+      s.commitEdit();
+      i = (Integer) s.getValue();
+    } catch (Exception e)
+    {
+      Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
+    }
+    return i;
+  }
+
+  private void keepRollMaxOptionsEnabled()
+  {
+    boolean enabled = backupfilesKeepAll.isEnabled()
+            && !backupfilesKeepAll.isSelected();
+    oldBackupFilesLabel.setEnabled(enabled);
+    backupfilesRollMaxSpinner.setEnabled(enabled);
+    backupfilesConfirmDelete.setEnabled(enabled);
+  }
+
+  private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
+  {
+    boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+            && customiseCheckbox.isSelected()
+            && suffixTemplate.getText()
+                    .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
+    keepfilesPanel.setEnabled(enabled);
+    backupfilesKeepAll.setEnabled(enabled);
+    oldBackupFilesLabel.setEnabled(enabled);
+    keepRollMaxOptionsEnabled();
+  }
+
+  private void backupfilesSuffixTemplateDigitsSetEnabled()
+  {
+    boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
+            .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
+    suffixDigitsLabel.setEnabled(enabled);
+    suffixDigitsSpinner.setEnabled(enabled);
+    suffixReverse.setEnabled(enabled);
+  }
+
+  private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
+  {
+    boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+            && customiseCheckbox.isSelected();
+    suffixPanel.setEnabled(enabled);
+    suffixTemplateLabel.setEnabled(enabled);
+    suffixTemplate.setEnabled(enabled);
+    backupfilesSuffixTemplateDigitsSetEnabled();
+  }
+
+  private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
+  {
+    boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+            && customiseCheckbox.isSelected() && backupfilesCustomChanged();
+    revertButton.setEnabled(enabled);
+  }
+
+  private boolean backupfilesCustomChanged()
+  {
+    BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+            .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+    BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
+    return !custom.equals(current);
+  }
+
+  protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
+  {
+    String suffix = suffixTemplate.getText();
+    int digits = getSpinnerInt(suffixDigitsSpinner, 3);
+    boolean reverse = suffixReverse.isSelected();
+    boolean keepAll = backupfilesKeepAll.isSelected();
+    int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
+    boolean confirmDelete = backupfilesConfirmDelete.isSelected();
+
+    BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
+            reverse, keepAll, rollMax, confirmDelete);
+
+    return bfpe;
+  }
+
+  protected void backupfilesCustomOptionsSetEnabled()
+  {
+    boolean enabled = customiseCheckbox.isSelected();
+
+    backupfilesRevertButtonSetEnabled(enabled);
+    backupfilesSuffixTemplateSetEnabled(enabled);
+    backupfilesKeepAllSetEnabled(enabled);
+  }
+
+  private void backupfilesSummarySetEnabled()
+  {
+    boolean enabled = enableBackupFiles.isSelected();
+    backupfilesExampleLabel.setEnabled(enabled);
+    exampleFilesPanel.setEnabled(enabled);
+  }
+
+  private void backupfilesPresetsSetEnabled()
+  {
+    boolean enabled = enableBackupFiles.isSelected();
+    presetsPanel.setEnabled(enabled);
+    presetsComboLabel.setEnabled(enabled);
+    backupfilesPresetsCombo.setEnabled(enabled);
+    customiseCheckbox.setEnabled(enabled);
+    revertButton.setEnabled(enabled);
+  }
+
+  protected void backupsOptionsSetEnabled()
+  {
+    backupfilesPresetsSetEnabled();
+    backupfilesSummarySetEnabled();
+    backupfilesCustomOptionsSetEnabled();
+  }
+
+  protected void backupsSetOptions(String suffix, int digits,
+          boolean reverse, boolean keepAll, int rollMax,
+          boolean confirmDelete)
+  {
+    suffixTemplate.setText(suffix);
+    suffixDigitsSpinner.setValue(digits);
+    suffixReverse.setSelected(reverse);
+    backupfilesKeepAll.setSelected(keepAll);
+    backupfilesRollMaxSpinner.setValue(rollMax);
+    backupfilesConfirmDelete.setSelected(confirmDelete);
+  }
+
+  protected void backupsSetOptions(BackupFilesPresetEntry p)
+  {
+    backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
+            p.confirmDelete);
+  }
+
+  protected void autoIdWidth_actionPerformed()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void userIdWidth_actionPerformed()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void maxColour_actionPerformed(JPanel panel)
+  {
+  }
+
+  protected void minColour_actionPerformed(JPanel panel)
+  {
+  }
+
+  protected void gapColour_actionPerformed(JPanel panel)
+  {
+  }
+
+  protected void hiddenColour_actionPerformed(JPanel panel)
+  {
+  }
+
+  protected void showunconserved_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void useLegacyGaps_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void resetOvDefaults_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void annotations_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void startupFileTextfield_mouseClicked()
+  {
+  }
+
+  public void newLink_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void editLink_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void deleteLink_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void defaultBrowser_mouseClicked(MouseEvent e)
+  {
+
+  }
+
+  public void linkURLList_keyTyped(KeyEvent e)
+  {
+
+  }
+
+  public void useProxy_actionPerformed()
+  {
+    boolean enabled = useProxy.isSelected();
+    portLabel.setEnabled(enabled);
+    serverLabel.setEnabled(enabled);
+    proxyServerTB.setEnabled(enabled);
+    proxyPortTB.setEnabled(enabled);
+  }
+
+  /**
+   * Customer renderer for JTable: supports column of radio buttons
+   */
+  public class RadioButtonRenderer extends JRadioButton
+          implements TableCellRenderer
+  {
+    public RadioButtonRenderer()
+    {
+      setHorizontalAlignment(CENTER);
       setToolTipText(MessageManager.getString("label.urltooltip"));
     }
 
@@ -1803,8 +3038,40 @@ public class GPreferences extends JPanel
 
   }
 
-  public void hmmerPath_actionPerformed(ActionEvent e)
+  protected void validateHmmerPath()
   {
+  }
 
+  protected void validateCygwinPath()
+  {
+  }
+
+  /**
+   * A helper method to add a panel containing a label and a component to a
+   * panel
+   * 
+   * @param panel
+   * @param tooltip
+   * @param label
+   * @param valBox
+   */
+  protected static void addtoLayout(JPanel panel, String tooltip,
+          JComponent label, JComponent valBox)
+  {
+    JPanel laypanel = new JPanel(new GridLayout(1, 2));
+    JPanel labPanel = new JPanel(new BorderLayout());
+    JPanel valPanel = new JPanel();
+    labPanel.setBounds(new Rectangle(7, 7, 158, 23));
+    valPanel.setBounds(new Rectangle(172, 7, 270, 23));
+    labPanel.add(label, BorderLayout.WEST);
+    valPanel.add(valBox);
+    laypanel.add(labPanel);
+    laypanel.add(valPanel);
+    valPanel.setToolTipText(tooltip);
+    labPanel.setToolTipText(tooltip);
+    valBox.setToolTipText(tooltip);
+    panel.add(laypanel);
+    panel.validate();
   }
 }
+