X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=4e909f1812268b2a9ea232aeccca74cf6cc89932;hb=7692386ccfe778075dd83a753d30a7a27fe507be;hp=bb6f22384f7706861b1ed0b72cb2ad889ce4b183;hpb=cef7be0f9008ff15318e3479a5de35e127071ef3;p=jalview.git

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index bb6f223..4e909f1 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -26,6 +26,7 @@ import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -40,7 +41,6 @@ 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.MouseAdapter;
 import java.awt.event.MouseEvent;
@@ -48,11 +48,13 @@ import java.awt.event.MouseEvent;
 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;
@@ -72,6 +74,8 @@ 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.
  * 
@@ -187,6 +191,19 @@ 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();
@@ -260,34 +277,19 @@ public class GPreferences extends JPanel
   /*
    * hmmer tab and components
    */
-  protected JPanel hmmerTab = new JPanel();
-
-  protected JCheckBox trimTermini = new JCheckBox();
-
-  protected ButtonGroup backgroundFreqSource = new ButtonGroup();
+  protected JPanel hmmerTab;
 
-  protected AbstractButton uniprot = new JCheckBox();
+  protected JCheckBox hmmrTrimTermini;
 
-  protected AbstractButton alignment = new JCheckBox();
+  protected AbstractButton hmmerBackgroundUniprot;
 
-  protected JLabel sequencesToKeep = new JLabel();
+  protected AbstractButton hmmerBackgroundAlignment;
 
-  protected JTextField numberOfSequencesToKeepField = new JTextField();
+  protected JTextField hmmerSequenceCount;
 
-  protected JLabel installationLocation = new JLabel();
+  protected JTextField hmmerPath;
 
-  protected JCheckBox isHMMERInstalled = new JCheckBox();
-
-  protected JTextField hmmerPath = new JTextField();
-
-  protected JLabel hmmsearch = new JLabel();
-
-  protected JLabel hmmalign = new JLabel();
-
-  /*
-   * DAS Settings tab
-   */
-  protected JPanel dasTab = new JPanel();
+  protected JTextField cygwinPath;
 
   /*
    * Web Services tab
@@ -329,6 +331,9 @@ 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"));
 
@@ -347,12 +352,6 @@ 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());
@@ -360,7 +359,7 @@ public class GPreferences extends JPanel
 
     /*
      * Handler to validate a tab before leaving it - currently only for
-     * Structure.
+     * Structure
      */
     tabbedPane.addChangeListener(new ChangeListener()
     {
@@ -378,16 +377,6 @@ 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 +413,29 @@ public class GPreferences extends JPanel
   }
 
   /**
-   * Initialises the hmmer tabbed panel.
+   * Initialises the hmmer tabbed panel
    * 
    * @return
    */
   private JPanel initHMMERTab()
   {
-    hmmerTab.setLayout(null);
+    hmmerTab = new JPanel();
+    hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS));
+    hmmerTab.setLayout(new MigLayout("flowy"));
 
-    hmmalign.setFont(LABEL_FONT);
-    hmmalign.setText(MessageManager.getString("label.hmmalign_label"));
-    hmmalign.setBounds(new Rectangle(22, 10, 200, 23));
-
-    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 +447,95 @@ public class GPreferences extends JPanel
           if (chosen != null)
           {
             hmmerPath.setText(chosen);
+            validateHmmerPath();
           }
         }
       }
     });
+    installationPanel.add(hmmerLocation);
+    installationPanel.add(hmmerPath);
 
-    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);
+    /*
+     * path to Cygwin binaries folder (for Windows)
+     */
+    if (Platform.isWindows())
+    {
+      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);
+    }
+
+    /*
+     * 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;
   }
@@ -644,7 +672,9 @@ 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
@@ -1065,7 +1095,7 @@ 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 +1107,7 @@ 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 +1116,11 @@ 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 +1129,151 @@ 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 +1356,14 @@ 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()
     {
@@ -1275,46 +1450,11 @@ 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 +1651,9 @@ 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
@@ -1654,12 +1797,28 @@ public class GPreferences extends JPanel
   {
   }
 
+  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!
    * 
@@ -1803,8 +1962,39 @@ 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();
   }
 }