X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGStructureChooser.java;h=e4e73d18f4038f857af017e5f8f11a3141c73155;hb=6849cc1cb983a45b4b8fd840f5ffc7d31ca80f33;hp=c4043c49539d80c6d1b6dd5993b1d47ca759d07e;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java
index c4043c4..e4e73d1 100644
--- a/src/jalview/jbgui/GStructureChooser.java
+++ b/src/jalview/jbgui/GStructureChooser.java
@@ -22,24 +22,32 @@
 package jalview.jbgui;
 
 import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
+import jalview.gui.JvSummaryTable;
 import jalview.gui.JvSwingUtils;
-import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
 import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
 
 import java.awt.BorderLayout;
 import java.awt.CardLayout;
+import java.awt.Component;
 import java.awt.Dimension;
 import java.awt.FlowLayout;
+import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
 
 import javax.swing.ImageIcon;
 import javax.swing.JButton;
@@ -48,15 +56,19 @@ import javax.swing.JComboBox;
 import javax.swing.JFrame;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
+import javax.swing.JList;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
+import javax.swing.JSeparator;
 import javax.swing.JTabbedPane;
 import javax.swing.JTable;
 import javax.swing.JTextField;
+import javax.swing.ListCellRenderer;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 import javax.swing.event.DocumentEvent;
 import javax.swing.event.DocumentListener;
+import javax.swing.event.InternalFrameEvent;
 
 @SuppressWarnings("serial")
 /**
@@ -67,6 +79,12 @@ import javax.swing.event.DocumentListener;
 public abstract class GStructureChooser extends JPanel implements
         ItemListener
 {
+  protected JPanel statusPanel = new JPanel();
+
+  public JLabel statusBar = new JLabel();
+
+  private JPanel pnl_actionsAndStatus = new JPanel(new BorderLayout());
+
   protected String frameTitle = MessageManager
           .getString("label.structure_chooser");
 
@@ -87,6 +105,8 @@ public abstract class GStructureChooser extends JPanel implements
 
   protected JButton btn_pdbFromFile = new JButton();
 
+  protected JButton btn_runPhyre2Prediction = new JButton();
+
   protected JTextField txt_search = new JTextField(14);
 
   private JPanel pnl_actions = new JPanel();
@@ -97,6 +117,10 @@ public abstract class GStructureChooser extends JPanel implements
 
   private JPanel pnl_fileChooser = new JPanel(new FlowLayout());
 
+  private JPanel pnl_phyre2Prediction = new JPanel(new FlowLayout());
+
+  private JPanel pnl_phyre2PredictionBL = new JPanel(new BorderLayout());
+
   private JPanel pnl_idInputBL = new JPanel(new BorderLayout());
 
   private JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
@@ -136,6 +160,8 @@ public abstract class GStructureChooser extends JPanel implements
 
   protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
 
+  protected AssciateSeqPanel phyre2InputAssSeqPanel = new AssciateSeqPanel();
+
   protected AssciateSeqPanel idInputAssSeqPanel = new AssciateSeqPanel();
 
   protected AssciateSeqPanel fileChooserAssSeqPanel = new AssciateSeqPanel();
@@ -148,43 +174,35 @@ public abstract class GStructureChooser extends JPanel implements
 
   protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
 
-  protected JTable tbl_summary = new JTable()
-  {
-    public String getToolTipText(MouseEvent evt)
-    {
-      String toolTipText = null;
-      java.awt.Point pnt = evt.getPoint();
-      int rowIndex = rowAtPoint(pnt);
-      int colIndex = columnAtPoint(pnt);
-
-      try
-      {
-        toolTipText = getValueAt(rowIndex, colIndex).toString();
-      } catch (Exception e)
-      {
-        e.printStackTrace();
-      }
-      toolTipText = (toolTipText == null ? null
-              : (toolTipText.length() > 500 ? JvSwingUtils.wrapTooltip(
-                      true, "\"" + toolTipText.subSequence(0, 500)
-                              + "...\"") : JvSwingUtils.wrapTooltip(true,
-                      toolTipText)));
-      return toolTipText;
-    }
-  };
-
-  protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
+  protected static final String VIEWS_PHYRE2_PREDICTION = "VIEWS_PHYRE2_PREDICTION";
 
   protected JTable tbl_local_pdb = new JTable();
 
   protected JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
 
-  private JTabbedPane pnl_filter = new JTabbedPane();
+  protected JTabbedPane pnl_filter = new JTabbedPane();
+
+  protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
+          PreferenceSource.STRUCTURE_CHOOSER,
+          PDBFTSRestClient.getInstance());
+
+  protected FTSDataColumnI[] previousWantedFields;
+
+  protected static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+
+  private JTable tbl_summary = new JvSummaryTable(tempUserPrefs);
+
+
+  protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
+
+  JPanel phyreResultPanel = new JPanel(new BorderLayout());
+  
+  protected static Map<String, Integer> tempPrefsForPhyre = new HashMap<String, Integer>();
 
-  private PDBDocFieldPreferences pdbDocFieldPrefs = new PDBDocFieldPreferences(
-          PreferenceSource.STRUCTURE_CHOOSER);
+  private JTable tbl_phyre2_summary = new JvSummaryTable(tempPrefsForPhyre);
 
-  protected PDBDocField[] previousWantedFields;
+  protected JScrollPane scrl_phyre2Summary = new JScrollPane(
+          tbl_phyre2_summary);
 
   public GStructureChooser()
   {
@@ -205,41 +223,159 @@ public abstract class GStructureChooser extends JPanel implements
    * 
    * @throws Exception
    */
+  @SuppressWarnings("unchecked")
   private void jbInit() throws Exception
   {
+    Integer width = tempUserPrefs.get("structureChooser.width") == null ? 800
+            : tempUserPrefs.get("structureChooser.width");
+    Integer height = tempUserPrefs.get("structureChooser.height") == null ? 400
+            : tempUserPrefs.get("structureChooser.height");
     tbl_summary.setAutoCreateRowSorter(true);
     tbl_summary.getTableHeader().setReorderingAllowed(false);
+    tbl_summary.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mouseClicked(MouseEvent e)
+      {
+        validateSelections();
+      }
+
+      @Override
+      public void mouseReleased(MouseEvent e)
+      {
+        validateSelections();
+      }
+    });
+    tbl_summary.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent evt)
+      {
+        validateSelections();
+        switch (evt.getKeyCode())
+        {
+        case KeyEvent.VK_ESCAPE: // escape key
+          mainFrame.dispose();
+          break;
+        case KeyEvent.VK_ENTER: // enter key
+          if (btn_view.isEnabled())
+          {
+            ok_ActionPerformed();
+          }
+          break;
+        case KeyEvent.VK_TAB: // tab key
+          if (evt.isShiftDown())
+          {
+            pnl_filter.requestFocus();
+          }
+          else
+          {
+            btn_view.requestFocus();
+          }
+          evt.consume();
+          break;
+        default:
+          return;
+        }
+      }
+    });
     tbl_local_pdb.setAutoCreateRowSorter(true);
     tbl_local_pdb.getTableHeader().setReorderingAllowed(false);
     tbl_local_pdb.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mouseClicked(MouseEvent e)
       {
-        updateCurrentView();
+        validateSelections();
       }
 
+      @Override
       public void mouseReleased(MouseEvent e)
       {
-        updateCurrentView();
+        validateSelections();
+      }
+    });
+    tbl_local_pdb.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent evt)
+      {
+        validateSelections();
+        switch (evt.getKeyCode())
+        {
+        case KeyEvent.VK_ESCAPE: // escape key
+          mainFrame.dispose();
+          break;
+        case KeyEvent.VK_ENTER: // enter key
+          if (btn_view.isEnabled())
+          {
+            ok_ActionPerformed();
+          }
+          break;
+        case KeyEvent.VK_TAB: // tab key
+          if (evt.isShiftDown())
+          {
+            cmb_filterOption.requestFocus();
+          }
+          else
+          {
+            if (btn_view.isEnabled())
+            {
+              btn_view.requestFocus();
+            }
+            else
+            {
+              btn_cancel.requestFocus();
+            }
+          }
+          evt.consume();
+          break;
+        default:
+          return;
+        }
       }
     });
-
     btn_view.setFont(new java.awt.Font("Verdana", 0, 12));
     btn_view.setText(MessageManager.getString("action.view"));
     btn_view.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         ok_ActionPerformed();
       }
     });
+    btn_view.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent evt)
+      {
+        if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+        {
+          ok_ActionPerformed();
+        }
+      }
+    });
+
     btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
     btn_cancel.setText(MessageManager.getString("action.cancel"));
     btn_cancel.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        mainFrame.dispose();
+        closeAction(pnl_filter.getHeight());
+      }
+    });
+    btn_cancel.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent evt)
+      {
+        if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+        {
+          closeAction(pnl_filter.getHeight());
+        }
       }
     });
 
@@ -248,17 +384,111 @@ public abstract class GStructureChooser extends JPanel implements
     btn_pdbFromFile.setText(btn_title + "              ");
     btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         pdbFromFile_actionPerformed();
       }
     });
+    btn_pdbFromFile.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent evt)
+      {
+        if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+        {
+          pdbFromFile_actionPerformed();
+        }
+      }
+    });
 
-    scrl_foundStructures.setPreferredSize(new Dimension(500, 300));
-    scrl_foundStructures
-            .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+    btn_pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12));
+    tbl_phyre2_summary.setAutoCreateRowSorter(true);
+    tbl_phyre2_summary.getTableHeader().setReorderingAllowed(false);
+
+    tbl_phyre2_summary.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mouseClicked(MouseEvent e)
+      {
+        validateSelections();
+      }
+
+      @Override
+      public void mouseReleased(MouseEvent e)
+      {
+        validateSelections();
+      }
+    });
+    tbl_phyre2_summary.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent evt)
+      {
+        validateSelections();
+        switch (evt.getKeyCode())
+        {
+        case KeyEvent.VK_ESCAPE: // escape key
+          mainFrame.dispose();
+          break;
+        case KeyEvent.VK_ENTER: // enter key
+          if (btn_view.isEnabled())
+          {
+            ok_ActionPerformed();
+          }
+          break;
+        case KeyEvent.VK_TAB: // tab key
+          if (evt.isShiftDown())
+          {
+            cmb_filterOption.requestFocus();
+          }
+          else
+          {
+            if (btn_view.isEnabled())
+            {
+              btn_view.requestFocus();
+            }
+            else
+            {
+              btn_cancel.requestFocus();
+            }
+          }
+          evt.consume();
+          break;
+        default:
+          return;
+        }
+      }
+    });
 
-    scrl_localPDB.setPreferredSize(new Dimension(500, 300));
+    String btn_runPhyre2Prediction_title = MessageManager
+            .getString("label.run_phyre2_prediction");
+    btn_runPhyre2Prediction
+            .setText(btn_runPhyre2Prediction_title + "     ");
+    btn_runPhyre2Prediction
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                predict3DModelWithPhyre2();
+              }
+            });
+    btn_runPhyre2Prediction.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent evt)
+      {
+        if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+        {
+          predict3DModelWithPhyre2();
+        }
+      }
+    });
+
+    scrl_foundStructures.setPreferredSize(new Dimension(width, height));
+
+    scrl_localPDB.setPreferredSize(new Dimension(width, height));
     scrl_localPDB
             .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 
@@ -266,9 +496,8 @@ public abstract class GStructureChooser extends JPanel implements
     chk_invertFilter.setFont(new java.awt.Font("Verdana", 0, 12));
     chk_rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12));
     chk_rememberSettings.setVisible(false);
-
-    txt_search.setToolTipText(MessageManager
-            .getString("label.enter_pdb_id"));
+    txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.enter_pdb_id")));
     cmb_filterOption.setToolTipText(MessageManager
             .getString("info.select_filter_option"));
     txt_search.getDocument().addDocumentListener(new DocumentListener()
@@ -293,6 +522,19 @@ public abstract class GStructureChooser extends JPanel implements
     });
 
     cmb_filterOption.addItemListener(this);
+
+    // add CustomComboSeparatorsRenderer to filter option combo-box
+    cmb_filterOption.setRenderer(new CustomComboSeparatorsRenderer(
+            (ListCellRenderer<Object>) cmb_filterOption.getRenderer())
+    {
+      @Override
+      protected boolean addSeparatorAfter(JList list, FilterOption value,
+              int index)
+      {
+        return value.isAddSeparatorAfter();
+      }
+    });
+
     chk_invertFilter.addItemListener(this);
 
     pnl_actions.add(chk_rememberSettings);
@@ -310,6 +552,17 @@ public abstract class GStructureChooser extends JPanel implements
     pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
     pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER);
 
+    scrl_phyre2Summary.setPreferredSize(new Dimension(width, height));
+    scrl_phyre2Summary
+            .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+
+    phyreResultPanel.add(pnl_phyre2Prediction, BorderLayout.NORTH);
+    phyreResultPanel.add(scrl_phyre2Summary, BorderLayout.CENTER);
+
+    pnl_phyre2Prediction.add(btn_runPhyre2Prediction);
+    pnl_phyre2PredictionBL.add(phyre2InputAssSeqPanel, BorderLayout.NORTH);
+    pnl_phyre2PredictionBL.add(phyreResultPanel, BorderLayout.CENTER);
+
     pnl_idInput.add(txt_search);
     pnl_idInput.add(lbl_pdbManualFetchStatus);
     pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
@@ -321,18 +574,23 @@ public abstract class GStructureChooser extends JPanel implements
             .getString("label.configure_displayed_columns");
     ChangeListener changeListener = new ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent changeEvent)
       {
         JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
                 .getSource();
         int index = sourceTabbedPane.getSelectedIndex();
+        btn_view.setVisible(true);
+        btn_cancel.setVisible(true);
         if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
         {
           btn_view.setEnabled(false);
           btn_cancel.setEnabled(false);
-          previousWantedFields = PDBDocFieldPreferences
+          btn_view.setVisible(false);
+          btn_cancel.setVisible(false);
+          previousWantedFields = pdbDocFieldPrefs
                   .getStructureSummaryFields().toArray(
-                          new PDBRestClient.PDBDocField[0]);
+                          new FTSDataColumnI[0]);
         }
         if (sourceTabbedPane.getTitleAt(index)
                 .equals(foundStructureSummary))
@@ -350,7 +608,7 @@ public abstract class GStructureChooser extends JPanel implements
       }
     };
     pnl_filter.addChangeListener(changeListener);
-    pnl_filter.setPreferredSize(new Dimension(500, 300));
+    pnl_filter.setPreferredSize(new Dimension(width, height));
     pnl_filter.add(foundStructureSummary, scrl_foundStructures);
     pnl_filter.add(configureCols, pdbDocFieldPrefs);
 
@@ -360,16 +618,48 @@ public abstract class GStructureChooser extends JPanel implements
     pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
     pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
     pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
+    pnl_switchableViews
+            .add(pnl_phyre2PredictionBL, VIEWS_PHYRE2_PREDICTION);
 
     this.setLayout(mainLayout);
     this.add(pnl_main, java.awt.BorderLayout.NORTH);
     this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
-    this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
-
+    // this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
+    statusPanel.setLayout(new GridLayout());
+    pnl_actionsAndStatus.add(pnl_actions, BorderLayout.CENTER);
+    pnl_actionsAndStatus.add(statusPanel, BorderLayout.SOUTH);
+    statusPanel.add(statusBar, null);
+    this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH);
+
+    mainFrame
+            .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+              @Override
+              public void internalFrameClosing(InternalFrameEvent e)
+              {
+                closeAction(pnl_filter.getHeight());
+              }
+            });
     mainFrame.setVisible(true);
     mainFrame.setContentPane(this);
     mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
-    Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
+    Integer x = tempUserPrefs.get("structureChooser.x");
+    Integer y = tempUserPrefs.get("structureChooser.y");
+    if (x != null && y != null)
+    {
+      mainFrame.setLocation(x, y);
+    }
+    Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
+  }
+
+  protected void closeAction(int preferredHeight)
+  {
+    tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth());
+    tempUserPrefs.put("structureChooser.height",
+            pnl_filter.getHeight() - 76);
+    tempUserPrefs.put("structureChooser.x", mainFrame.getX());
+    tempUserPrefs.put("structureChooser.y", mainFrame.getY());
+    mainFrame.dispose();
   }
 
   public boolean wantedFieldsUpdated()
@@ -379,9 +669,10 @@ public abstract class GStructureChooser extends JPanel implements
       return true;
     }
 
-    return Arrays.equals(PDBDocFieldPreferences.getStructureSummaryFields()
-            .toArray(new PDBRestClient.PDBDocField[0]),
-            previousWantedFields) ? false : true;
+    FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs
+            .getStructureSummaryFields().toArray(new FTSDataColumnI[0]);
+    return Arrays.equals(currentWantedFields, previousWantedFields) ? false
+            : true;
 
   }
 
@@ -408,11 +699,15 @@ public abstract class GStructureChooser extends JPanel implements
 
     private String view;
 
-    public FilterOption(String name, String value, String view)
+    private boolean addSeparatorAfter;
+
+    public FilterOption(String name, String value, String view,
+            boolean addSeparatorAfter)
     {
       this.name = name;
       this.value = value;
       this.view = view;
+      this.addSeparatorAfter = addSeparatorAfter;
     }
 
     public String getName()
@@ -445,10 +740,21 @@ public abstract class GStructureChooser extends JPanel implements
       this.view = view;
     }
 
+    @Override
     public String toString()
     {
       return this.name;
     }
+
+    public boolean isAddSeparatorAfter()
+    {
+      return addSeparatorAfter;
+    }
+
+    public void setAddSeparatorAfter(boolean addSeparatorAfter)
+    {
+      this.addSeparatorAfter = addSeparatorAfter;
+    }
   }
 
   /**
@@ -477,6 +783,7 @@ public abstract class GStructureChooser extends JPanel implements
       this.sequence = seq;
     }
 
+    @Override
     public String toString()
     {
       return name;
@@ -553,16 +860,64 @@ public abstract class GStructureChooser extends JPanel implements
     }
   }
 
+  public JTable getResultTable()
+  {
+    return tbl_summary;
+  }
+
   public JComboBox<FilterOption> getCmbFilterOption()
   {
     return cmb_filterOption;
   }
 
-  protected abstract void stateChanged(ItemEvent e);
 
-  protected abstract void updateCurrentView();
+  public JTable getPhyreResultTable()
+  {
+    return tbl_phyre2_summary;
+  }
+
+  public abstract class CustomComboSeparatorsRenderer implements
+          ListCellRenderer<Object>
+  {
+    private ListCellRenderer<Object> regent;
+
+    private JPanel separatorPanel = new JPanel(new BorderLayout());
+
+    private JSeparator jSeparator = new JSeparator();
+
+    public CustomComboSeparatorsRenderer(ListCellRenderer<Object> listCellRenderer)
+    {
+      this.regent = listCellRenderer;
+    }
+
+    @Override
+    public Component getListCellRendererComponent(JList list,
+            Object value,
+            int index, boolean isSelected, boolean cellHasFocus)
+    {
 
-  protected abstract void populateFilterComboBox();
+      Component comp = regent.getListCellRendererComponent(list, value,
+              index, isSelected, cellHasFocus);
+      if (index != -1
+              && addSeparatorAfter(list, (FilterOption) value, index))
+      { 
+        separatorPanel.removeAll();
+        separatorPanel.add(comp, BorderLayout.CENTER);
+        separatorPanel.add(jSeparator, BorderLayout.SOUTH);
+        return separatorPanel;
+      }
+      else
+      {
+        return comp;
+      }
+    }
+
+    protected abstract boolean addSeparatorAfter(JList list,
+            FilterOption value,
+            int index);
+  }
+
+  protected abstract void stateChanged(ItemEvent e);
 
   protected abstract void ok_ActionPerformed();
 
@@ -578,4 +933,7 @@ public abstract class GStructureChooser extends JPanel implements
   public abstract void tabRefresh();
 
   public abstract void validateSelections();
-}
+
+  public abstract void predict3DModelWithPhyre2();
+
+}
\ No newline at end of file