FitnessParametersForm.java

Go to the documentation of this file.

/*
 *   DENOPTIM
 *   Copyright (C) 2020 Marco Foscato <marco.foscato@uib.no>
 *
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU Affero General Public License as published
 *   by the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU Affero General Public License for more details.
 *
 *   You should have received a copy of the GNU Affero General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
package denoptim.gui;
 
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.atomic.AtomicInteger;
 
import javax.swing.BoxLayout;
import javax.swing.GroupLayout;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JEditorPane;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JSplitPane;
import javax.swing.JTable;
import javax.swing.JTextField;
import javax.swing.JTree;
import javax.swing.SwingConstants;
import javax.swing.UIManager;
import javax.swing.event.TreeSelectionEvent;
import javax.swing.event.TreeSelectionListener;
import javax.swing.table.DefaultTableModel;
import javax.swing.table.JTableHeader;
import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.DefaultTreeCellRenderer;
import javax.swing.tree.DefaultTreeModel;
import javax.swing.tree.TreePath;
 
import org.openscience.cdk.fingerprint.IBitFingerprint;
import org.openscience.cdk.fingerprint.IFingerprinter;
import org.openscience.cdk.qsar.IDescriptor;
 
import denoptim.exception.DENOPTIMException;
import denoptim.fitness.DescriptorForFitness;
import denoptim.fitness.DescriptorUtils;
import denoptim.programs.RunTimeParameters;
 
public class FitnessParametersForm extends ParametersForm
{
 
    private static final long serialVersionUID = -282726238111247056L;
    
    public static AtomicInteger fitFormUID = new AtomicInteger(1);
    
    private Map<String,Object> mapKeyFieldToValueField;
    
    JPanel block;    
    JPanel localBlock1;
    JPanel localBlock2;
    JPanel localBlock3;
    JPanel localBlock4;
    
    JPanel lineSrcOrNew;
    JRadioButton rdbSrcOrNew;
    
    String key3dTrees = "FP-No3dTreeModel";
    JPanel line3dTrees;
    JRadioButton rdb3dTrees;
    
    String keyPreFitnessUIDCheck = "FP-CheckUidBeforeFitness";
    JPanel linePreFitnessUIDCheck;
    JRadioButton rdbPreFitnessUIDCheck;
    
    JPanel lineFPSource;
    JLabel lblFPSource;
    JTextField txtFPSource;
    JButton btnFPSource;
    JButton btnLoadFPSource;
    
    JPanel lineIntOrExt;
    JRadioButton rdbIntOrExt;
 
    String keyFitProviderSource = "FP-Source";
    JPanel lineFitProviderSource;
    JLabel lblFitProviderSource;
    JTextField txtFitProviderSource;
    JButton btnFitProviderSource;
 
    String keyFitProviderInterpreter = "FP-Interpreter";
    JPanel lineFitProviderInterpreter;
    JLabel lblFitProviderInterpreter;
    JTextField txtFitProviderInterpreter;
 
    String keyEq = "FP-Equation";
    JPanel lineEq;
    JLabel lblEq;
    JTextField txtEq;
    
    String keyCustomVars = "FP-DescriptorSpecs";
    JPanel lineCustomVars;
    JLabel lblCustomvars;
    JTable tabCustomVars;
    DefaultTableModel tabCustomVarsMod;
    
    JPanel descDefinitionPane;
    JScrollPane descDefScrollPane;
    JLabel lblDDValueTitle;
    JLabel lblDDValueName;
    JLabel lblDDValueDefinition;
    JLabel lblDDValueDescripton;
    JLabel lblDDValueClasses;
    JPanel pnlDDValueParams;
    JLabel lblDDValueParams;
    JButton btnDDValueParams;
    private String descNameToTune = "";
    private String[] paramsToTune;
    JLabel lblDDValueSource;
 
    //HEREGOFIELDS  this is only to facilitate automated insertion of code
        
    private static  Map<Class<?>,String> additionalDocForParameters;
    static {
        additionalDocForParameters = new HashMap<Class<?>,String>();
        Class<?> key = IBitFingerprint.class;
        additionalDocForParameters.put(key,
                "<p>The <code>" + key.getSimpleName() + "</code> parameter can "
                + "be generated "
                + "when importing the descriptor into the fitness provider. "
                + "To this end, use the prefix '<code>FILE:</code>' to "
                + "provide a pathname to an SDF file from which the "
                + "reference molecule can be fetched, and its fingerprint "
                + "calculated and finally used as parameter to configure "
                + "this descriptor.</p>");
        key = IFingerprinter.class;
        additionalDocForParameters.put(key,
                "<p>The <code>" + key.getSimpleName() 
                + "</code> parameter should be specified "
                + "as the simple name of the desired implementation. For "
                + "example <code>PubchemFingerprinter</code>. See "
                + "CDK documentation on IFingerprinter for available "
                + "implementations.</p>");
    }       
        
    String NL = System.getProperty("line.separator");
    
//------------------------------------------------------------------------------
    
    public FitnessParametersForm(Dimension d)
    {
        mapKeyFieldToValueField = new HashMap<String,Object>();
        
        this.setLayout(new BorderLayout()); //Needed to allow dynamic resizing!
 
        block = new JPanel();
        JScrollPane scrollablePane = new JScrollPane(block);
        block.setLayout(new BoxLayout(block, SwingConstants.VERTICAL));    
 
        localBlock1 = new JPanel();
        localBlock1.setVisible(false);
        localBlock1.setLayout(new BoxLayout(localBlock1, 
                SwingConstants.VERTICAL));
        
        localBlock2 = new JPanel();
        localBlock2.setVisible(true);
        localBlock2.setLayout(new BoxLayout(localBlock2, 
                SwingConstants.VERTICAL));
        
        localBlock3 = new JPanel();
        localBlock3.setVisible(false);
        localBlock3.setLayout(new BoxLayout(localBlock3, 
                SwingConstants.VERTICAL));
        
        localBlock4 = new JPanel();
        localBlock4.setVisible(true);
        localBlock4.setLayout(new BoxLayout(localBlock4, 
                SwingConstants.VERTICAL));
        
        String toolTipSrcOrNew = "Tick here to use settings from file.";
        lineSrcOrNew = new JPanel(new FlowLayout(FlowLayout.LEFT));
        rdbSrcOrNew = new JRadioButton("Use parameters from existing file");
        rdbSrcOrNew.setToolTipText(toolTipSrcOrNew);
        rdbSrcOrNew.addActionListener(new ActionListener(){
            public void actionPerformed(ActionEvent e){
                if (rdbSrcOrNew.isSelected())
                {
                    localBlock1.setVisible(true);
                    localBlock2.setVisible(false);
                }
                else
                {
                    localBlock1.setVisible(false);
                    localBlock2.setVisible(true);
                }
            }
        });
        lineSrcOrNew.add(rdbSrcOrNew);
        block.add(lineSrcOrNew);
        block.add(localBlock1);
        block.add(localBlock2);
        
        String toolTipFPSource = "<html>Pathname of a DENOPTIM's parameter "
                + "file with fitness-provider settings.</html>";
        lineFPSource = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblFPSource = new JLabel("Use parameters from file:", 
                SwingConstants.LEFT);
        lblFPSource.setToolTipText(toolTipFPSource);
        txtFPSource = new JTextField();
        txtFPSource.setToolTipText(toolTipFPSource);
        txtFPSource.setPreferredSize(fileFieldSize);
        btnFPSource = new JButton("Browse");
        btnFPSource.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
                GUIFileOpener.pickFileForTxtField(txtFPSource,
                        btnFPSource);
           }
        });
        btnLoadFPSource = new JButton("Load...");
        txtFPSource.setToolTipText("<html>Specify the file containing the "
                + "parameters to be loaded in this form.</html>");
        btnLoadFPSource.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                try 
                {
                    importParametersFromDenoptimParamsFile(
                            txtFPSource.getText());
                } 
                catch (Exception e1) 
                {
                    if (e1.getMessage().equals("") || e1.getMessage() == null)
                    {
                        e1.printStackTrace();
                        JOptionPane.showMessageDialog(btnLoadFPSource,
                                "<html>Exception occurred while importing "
                                + "parameters.<br>Please, report this to the "
                                + "DENOPTIM team.</html>",
                                "Error",
                                JOptionPane.ERROR_MESSAGE,
                                UIManager.getIcon("OptionPane.errorIcon"));
                    }
                    else
                    {
                        JOptionPane.showMessageDialog(btnLoadFPSource,
                                e1.getMessage(),
                                "Error",
                                JOptionPane.ERROR_MESSAGE,
                                UIManager.getIcon("OptionPane.errorIcon"));
                    }
                    return;
                }
            }
        });
        lineFPSource.add(lblFPSource);
        lineFPSource.add(txtFPSource);
        lineFPSource.add(btnFPSource);
        lineFPSource.add(btnLoadFPSource);
        localBlock1.add(lineFPSource);
        
        
        String toolTip3dTrees = "<html>Tick here to enable/disable preliminary "
                + "generation of a unrefined<br>3D geometry prior to fitness "
                + "evaluation.<br>These models are build by aligning the given "
                + "3D fragments<br> to the attachment point vectors. "
                + "These models are <br>not energy-refined.</html>";
        line3dTrees = new JPanel(new FlowLayout(FlowLayout.LEFT));
        rdb3dTrees = new JRadioButton("Make unrefined 3d model.");
        rdb3dTrees.setToolTipText(toolTip3dTrees);
        rdb3dTrees.setSelected(true);
        mapKeyFieldToValueField.put(key3dTrees.toUpperCase(), rdb3dTrees);
        line3dTrees.add(rdb3dTrees);
        localBlock2.add(line3dTrees);
        
        String toolTipPreFitnessUIDCheck = "<html>Tick here to enable/disable evaluation "
                + "of candidate uniqueness prior to submission of the fitness "
                + "evaluation.</html>";
        linePreFitnessUIDCheck = new JPanel(new FlowLayout(FlowLayout.LEFT));
        rdbPreFitnessUIDCheck = new JRadioButton("Check candidate uniqueness "
                + "before sending to fitness evaluation.");
        rdbPreFitnessUIDCheck.setToolTipText(toolTipPreFitnessUIDCheck);
        rdbPreFitnessUIDCheck.setSelected(true);
        mapKeyFieldToValueField.put(keyPreFitnessUIDCheck.toUpperCase(), rdbPreFitnessUIDCheck);
        linePreFitnessUIDCheck.add(rdbPreFitnessUIDCheck);
        localBlock2.add(linePreFitnessUIDCheck);
        
 
        String toolTipIntOrExt = "<html>A fitness provider is an existing "
                + "tool or script.<br> The fitness provider must produce an "
                + "output SDF file with the <code>&lt;FITNESS&gt;</code> or "
                + "<code>&lt;MOL_ERROR&gt;</code> tags.</html>";
        lineIntOrExt = new JPanel(new FlowLayout(FlowLayout.LEFT));
        rdbIntOrExt = new JRadioButton("Use external fitness provider");
        rdbIntOrExt.setToolTipText(toolTipIntOrExt);
        
        rdbIntOrExt.setSelected(false);
        rdbIntOrExt.setEnabled(true);
        
        rdbIntOrExt.addActionListener(new ActionListener(){
            public void actionPerformed(ActionEvent e){
                setVisibilityAccordingToFitnessProviderSelection();
            }
        });
        lineIntOrExt.add(rdbIntOrExt);
        localBlock2.add(lineIntOrExt);
        localBlock2.add(localBlock3);
        localBlock2.add(localBlock4);
 
        //HEREGOESIMPLEMENTATION this is only to facilitate automated insertion of code
 
        String toolTipFitProviderSource = "Pathname of the executable file.";
        lineFitProviderSource = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblFitProviderSource = new JLabel("Fitness provider executable:", 
                SwingConstants.LEFT);
        lblFitProviderSource.setPreferredSize(fileLabelSize);
        lblFitProviderSource.setToolTipText(toolTipFitProviderSource);
        txtFitProviderSource = new JTextField();
        txtFitProviderSource.setToolTipText(toolTipFitProviderSource);
        txtFitProviderSource.setPreferredSize(fileFieldSize);
        txtFitProviderSource.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyFitProviderSource.toUpperCase(), 
                txtFitProviderSource);
        btnFitProviderSource = new JButton("Browse");
        btnFitProviderSource.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
                GUIFileOpener.pickFileForTxtField(
                        txtFitProviderSource, btnFitProviderSource);
           }
        });
        lineFitProviderSource.add(lblFitProviderSource);
        lineFitProviderSource.add(txtFitProviderSource);
        lineFitProviderSource.add(btnFitProviderSource);
        localBlock3.add(lineFitProviderSource);
        
        String toolTipFitProviderInterpreter = "Interpreter to be used for the "
                + "fitness provider executable";
        lineFitProviderInterpreter = new JPanel(
                new FlowLayout(FlowLayout.LEFT));
        lblFitProviderInterpreter = new JLabel("Interpreter for fitnes "
                + "provider", SwingConstants.LEFT);
        lblFitProviderInterpreter.setPreferredSize(fileLabelSize);
        lblFitProviderInterpreter.setToolTipText(toolTipFitProviderInterpreter);
        txtFitProviderInterpreter = new JTextField("/bin/bash");
        txtFitProviderInterpreter.setToolTipText(toolTipFitProviderInterpreter);
        txtFitProviderInterpreter.setEnabled(true);
        txtFitProviderInterpreter.setPreferredSize(fileFieldSize);
        
        mapKeyFieldToValueField.put(keyFitProviderInterpreter.toUpperCase(), 
                txtFitProviderInterpreter);
        lineFitProviderInterpreter.add(lblFitProviderInterpreter);
        lineFitProviderInterpreter.add(txtFitProviderInterpreter);
        localBlock3.add(lineFitProviderInterpreter);
 
        String toolTipEq = "Define integrated fitness provider expression.";
        lineEq = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblEq = new JLabel("<html><i>Fitness = </i>${</html>", 
                SwingConstants.LEFT);
        JLabel lblEqEnd = new JLabel("<html>}</html>", SwingConstants.LEFT);
        //lblEq.setPreferredSize(fileLabelSize);
        lblEq.setToolTipText(toolTipEq);
        txtEq = new JTextField();
        txtEq.setToolTipText("<html>Type here the expression for computing the fitness value out of predefined<br>"
                + "descriptors and custom variables.<ul>"
                + "<li>Descriptors can be selected from the 'Available descriptors' section (below).</li>"
                + "<li>Custom variables, including atom-specific descriptors, can be defined in <br>"
                + "the 'Custom variables' section.</li></ul></html>");
        Dimension fitEqSize = new Dimension(700, 2*preferredHeight);
        txtEq.setPreferredSize(fitEqSize);
        txtEq.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyEq.toUpperCase(),txtEq);
        lineEq.add(lblEq);
        lineEq.add(txtEq);
        lineEq.add(lblEqEnd);
        localBlock4.add(lineEq);
        
        JLabel lblDescTreeTitle = new JLabel("Available descriptors:");
        JPanel lineDescTreeTitle = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lineDescTreeTitle.add(lblDescTreeTitle);
        localBlock4.add(lineDescTreeTitle);
        
        String toolTipDescs = "<html>To select descriptor names:"
                + "<ol><li>Browse the list of descriptors (double click to expand/reduce a node),"
                + "</li><li>Click on the name of the descriptor you want to select,"
                + "</li><li>Copy the selected name (<code>ctrl+C</code>/<code>command+C</code>), click in the fitness<br>"
                + "expression field, and paste (<code>ctrl+V</code><code>command+V</code>).</li>"
                + "</ol></html>";
        
        DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(
                "Descriptors");
        DefaultTreeModel treeModel = new DefaultTreeModel(rootNode);
        JTree descTree = new JTree(treeModel);
        DefaultTreeCellRenderer renderer = new DefaultTreeCellRenderer();
        renderer.setLeafIcon(null);
        descTree.setCellRenderer(renderer);
        descTree.setRootVisible(true);
        descTree.setShowsRootHandles(true);
        //NB: appearance depends on lookAndfeel. On Mac no lines, even if asked
        descTree.putClientProperty("JTree.lineStyle", "Angled");
        descTree.setToolTipText(toolTipDescs);
        int dValLength = 350;
        descTree.addTreeSelectionListener(new TreeSelectionListener() {
            @Override
            public void valueChanged(TreeSelectionEvent e) {
                TreePath selPath = e.getPath();
                DefaultMutableTreeNode selTreeNode = (DefaultMutableTreeNode) 
                        selPath.getLastPathComponent();
                if (!(selTreeNode instanceof DescriptorTreeNode)
                        || !selTreeNode.isLeaf())
                {
                    return;
                }
                DescriptorTreeNode selNode = (DescriptorTreeNode) selTreeNode;
                DescriptorForFitness dff = selNode.dff;
 
                String titStr = dff.getDictTitle();
                titStr = "<html><body width='%1s'>" + titStr + "</body></html>";
                lblDDValueTitle.setText(String.format(titStr, dValLength));
                lblDDValueName.setText(dff.getShortName());
                
                String defStr = dff.getDictDefinition();
                defStr = "<html><body width='%1s'>" + defStr + "</body></html>";
                lblDDValueDefinition.setText(String.format(defStr, dValLength));
                
                lblDDValueDescripton.setText("No additional descripton available");
 
                String clsStr = Arrays.toString(dff.getDictClasses());
                clsStr = "<html><body width='%1s'>" + clsStr + "</body></html>";
                lblDDValueClasses.setText(String.format(clsStr, dValLength));
                
                String parStr ="";
                IDescriptor iDesc = dff.getImplementation();
                String[] parNames = iDesc.getParameterNames();
                Object[] params = iDesc.getParameters();
                //NB: some classes return null to avoid adding a way to alter
                // the default parameters.
                ArrayList<Object> paramsTypes = new ArrayList<Object>();
                if (params == null)
                {
                    parStr = "Undeclared parameters. See source code.";
                } else {
                    for (int ip=0; ip<parNames.length; ip++)
                    {
                        if (ip>0)
                        {
                            parStr = parStr + "<br>";
                        }
                        Object parTyp = iDesc.getParameterType(parNames[ip]);
                        
                        String parTypStr = parTyp.getClass().getSimpleName();
                        if (parTyp instanceof Class<?>)
                        {
                            parTypStr = ((Class<?>) iDesc.getParameterType(
                                    parNames[ip])).getSimpleName();
                        }
                        parStr = parStr + parNames[ip] + " = (" 
                                + parTypStr + ") " + params[ip];
                        paramsTypes.add(parTyp);
                    }
                }
                descNameToTune = dff.getShortName();
                if (paramsTypes.size() == 0)
                {
                    btnDDValueParams.setEnabled(false);
                    btnDDValueParams.setVisible(false);
                    paramsToTune = new String[0];
                } else {
                    btnDDValueParams.setEnabled(true);
                    btnDDValueParams.setVisible(true);
                    paramsToTune = parNames;
                }
                for (Object parTypeExample : paramsTypes)
                {
                    String s = additionalDocForParameters.get(parTypeExample);
                    if (s != null)
                    {
                        parStr = parStr + "<p> </p>" + s;
                    }
                }
                parStr = "<html><body width='%1s'>" + parStr + "</body></html>";
                lblDDValueParams.setText(String.format(parStr, dValLength));
                
                String srcStr = dff.getClassName();
                srcStr = "<html><body width='%1s'>" + srcStr + "</body></html>";
                lblDDValueSource.setText(String.format(srcStr, dValLength));
                
            }
        });
        JScrollPane descTreeScrollPane = new JScrollPane(descTree);
        
        String[] sources = new String[] {"CDK", "DENOPTIM"};
        for (String source : sources)
        {
            DescriptorTreeNode sourceNode = new DescriptorTreeNode(source);
            rootNode.add(sourceNode);
            
            List<DescriptorForFitness> allDescs = null;
            try {
                switch (source)
                {
                    case "CDK":
                        allDescs = DescriptorUtils.findAllCDKDescriptors(
                                null);
                        break;
                    case "DENOPTIM":
                        allDescs = DescriptorUtils.findAllDENOPTIMDescriptors(
                                null);
                        break;
                }
            } catch (DENOPTIMException e1) {
                System.out.println("No descriptor implementation found in "
                        + "source '" + source + "'!");
                e1.printStackTrace();
                continue;
            }
        
            // First identify the main klasses (first layer)
            Map<String,DescriptorTreeNode> mainClassificationNodes = 
                    new HashMap<String,DescriptorTreeNode>();
            for (DescriptorForFitness dff : allDescs)
            {   
                String[] klasses = new String[]{"Unclassified"};
                if (dff.getDictClasses()!=null)
                {
                    klasses = dff.getDictClasses();
                }
                for (String kls : klasses)
                {
                    if (!mainClassificationNodes.containsKey(kls))
                    {
                        DescriptorTreeNode klassNode = new DescriptorTreeNode(
                                kls);
                        sourceNode.add(klassNode);
                        mainClassificationNodes.put(kls, klassNode);
                    }
                }
            }
        
            // Then populate each class
            for (String klass : mainClassificationNodes.keySet())
            {
                DescriptorTreeNode klassNode = mainClassificationNodes.get(
                        klass);
                Map<String,DescriptorTreeNode> descriptorNodes = 
                        new HashMap<String,DescriptorTreeNode>();
                for (DescriptorForFitness dff : allDescs)
                {
                    //TODO: check if getting the dictionary from 
                    // DictionaryDatabase allows to get also the description in 
                    // addition to definition
                    
                    // Decide if this descriptor goes under the present klass
                    List<String> klasses = new ArrayList<String>();
                    if (dff.getDictClasses() == null)
                    {
                        if (!klass.equals("Unclassified"))
                        {
                            continue;
                        } else {
                            klasses.add(klass);
                        }
                    } else {
                        klasses = new ArrayList<String>(
                                Arrays.asList(dff.getDictClasses()));
                    }
                    if (!klasses.contains(klass))
                    {
                        continue;
                    }
                    
                    // Identify parent node: either a klassNode or a descriptorNode
                    DescriptorTreeNode parentNode = klassNode;
                    if (dff.getImplementation().getDescriptorNames().length > 1)
                    {
                        String descriptorName = dff.getImplementation().getClass()
                                .getSimpleName();
                        if (!descriptorNodes.containsKey(descriptorName))
                        {
                            DescriptorTreeNode descNode = 
                                    new DescriptorTreeNode(descriptorName,dff);
                            parentNode.add(descNode);
                            descriptorNodes.put(descriptorName, descNode);
                        }
                        parentNode = descriptorNodes.get(descriptorName);
                    }
                    
                    // Finally make the node for the present desc-to-fitness
                    DescriptorTreeNode dtn = new DescriptorTreeNode(dff);
                    parentNode.add(dtn);
                }
            }
        }
        
        Dimension ddLabelsSize = new Dimension(100,30);
        JLabel lblDDTitle = new JLabel("<html><b>Title:</b></html>");
        lblDDTitle.setPreferredSize(ddLabelsSize);
        JLabel lblDDName = new JLabel("<html><b>Name:</b></html>");
        lblDDName.setPreferredSize(ddLabelsSize);
        JLabel lblDDDefinition = new JLabel("<html><b>Definition:</b></html>");
        lblDDDefinition.setPreferredSize(ddLabelsSize);
        JLabel lblDDDescription = new JLabel("<html><b>Description:</b></html>");
        lblDDDescription.setPreferredSize(ddLabelsSize);
        JLabel lblDDClasses = new JLabel("<html><b>Classification:</b></html>");
        lblDDClasses.setPreferredSize(ddLabelsSize);
        JLabel lblDDParams = new JLabel("<html><b>Parameters:</b></html>");
        lblDDParams.setPreferredSize(ddLabelsSize);
        JLabel lblDDSource = new JLabel("<html><b>Implementation:</b></html>");
        lblDDSource.setPreferredSize(ddLabelsSize);
        
        lblDDValueTitle = new JLabel();
        lblDDValueName = new JLabel();
        lblDDValueDefinition = new JLabel();
        lblDDValueDescripton = new JLabel();
        lblDDValueClasses = new JLabel();
        pnlDDValueParams = new JPanel();
        lblDDValueParams = new JLabel();
        btnDDValueParams = new JButton("Set parameters");
        btnDDValueParams.setEnabled(false);
        btnDDValueParams.setVisible(false);
        lblDDValueSource = new JLabel();
        
        btnDDValueParams.addActionListener(new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e)
            {
                ParametrizedDescriptorDefinition dialog = 
                        new ParametrizedDescriptorDefinition(descNameToTune,
                                paramsToTune, btnDDValueParams);
                if (dialog.result!=null)
                {
                    tabCustomVarsMod.addRow((Object[]) dialog.result);
                }
            }
        });
        
        GroupLayout lyoDescParamsPanel = new GroupLayout(pnlDDValueParams);
        pnlDDValueParams.setLayout(lyoDescParamsPanel);
        lyoDescParamsPanel.setAutoCreateGaps(true);
        lyoDescParamsPanel.setAutoCreateContainerGaps(true);
        lyoDescParamsPanel.setHorizontalGroup(
                lyoDescParamsPanel.createParallelGroup()
                    .addComponent(lblDDValueParams)
                    .addComponent(btnDDValueParams));
        lyoDescParamsPanel.setVerticalGroup(
                lyoDescParamsPanel.createSequentialGroup()
                    .addComponent(lblDDValueParams)
                    .addComponent(btnDDValueParams));
        
        descDefinitionPane = new JPanel();
        GroupLayout lyoDescDefPanel = new GroupLayout(descDefinitionPane);
        descDefinitionPane.setLayout(lyoDescDefPanel);
        lyoDescDefPanel.setAutoCreateGaps(true);
        lyoDescDefPanel.setAutoCreateContainerGaps(true);
        lyoDescDefPanel.setHorizontalGroup(lyoDescDefPanel.createSequentialGroup()
                    .addGroup(lyoDescDefPanel.createParallelGroup()
                            .addComponent(lblDDName)
                            .addComponent(lblDDTitle)
                            .addComponent(lblDDClasses)
                            .addComponent(lblDDDefinition)
                            //.addComponent(lblDDDescription)
                            .addComponent(lblDDParams)
                            .addComponent(lblDDSource)
                            )
                    .addGroup(lyoDescDefPanel.createParallelGroup()
                            .addComponent(lblDDValueName)
                            .addComponent(lblDDValueTitle)
                            .addComponent(lblDDValueClasses)
                            .addComponent(lblDDValueDefinition)
                            //.addComponent(lblDDValueDescripton)
                            .addComponent(pnlDDValueParams)
                            .addComponent(lblDDValueSource)
                            ));
        lyoDescDefPanel.setVerticalGroup(lyoDescDefPanel.createSequentialGroup()
                .addGroup(lyoDescDefPanel.createParallelGroup()
                        .addComponent(lblDDName)
                        .addComponent(lblDDValueName))
                .addGroup(lyoDescDefPanel.createParallelGroup()
                        .addComponent(lblDDTitle)
                        .addComponent(lblDDValueTitle))
                .addGroup(lyoDescDefPanel.createParallelGroup()
                        .addComponent(lblDDClasses)
                        .addComponent(lblDDValueClasses))
                .addGroup(lyoDescDefPanel.createParallelGroup()
                        .addComponent(lblDDDefinition)
                        .addComponent(lblDDValueDefinition))
        //        .addGroup(lyoDescDefPanel.createParallelGroup()
        //              .addComponent(lblDDDescription)
        //              .addComponent(lblDDValueDescripton))
                .addGroup(lyoDescDefPanel.createParallelGroup()
                        .addComponent(lblDDParams)
                        .addComponent(pnlDDValueParams))
                .addGroup(lyoDescDefPanel.createParallelGroup()
                        .addComponent(lblDDSource)
                        .addComponent(lblDDValueSource))
                );
 
        descDefScrollPane = new JScrollPane(descDefinitionPane);
        
        JSplitPane splitPaneDescs = new JSplitPane();
        splitPaneDescs.setOrientation(JSplitPane.HORIZONTAL_SPLIT);
        splitPaneDescs.setOneTouchExpandable(true);
        splitPaneDescs.setResizeWeight(0.5);
        splitPaneDescs.setLeftComponent(descTreeScrollPane);
        splitPaneDescs.setRightComponent(descDefScrollPane);
        JPanel lineDescsTree = new JPanel();
        lineDescsTree.setLayout(new BorderLayout(2,2));
        lineDescsTree.add(splitPaneDescs);
        localBlock4.add(lineDescsTree);
        
        lblCustomvars = new JLabel("Definition of custom variables:");
        JPanel lineMoreEqTitle = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lineMoreEqTitle.add(lblCustomvars);
        localBlock4.add(lineMoreEqTitle);
        
        String toolTipMoreEq = "<html>Define atom/bond specific descriptors.</html>";
        lineCustomVars = new JPanel();
        
        tabCustomVarsMod = new DefaultTableModel();
        tabCustomVarsMod.setColumnCount(2);
        String column_names[]= {"<html><b>Variable</b></html>", 
                "<html><b>Definition</b></html>"};
        tabCustomVarsMod.setColumnIdentifiers(column_names);
        tabCustomVars = new JTable(tabCustomVarsMod);
        tabCustomVars.setToolTipText(toolTipMoreEq);
        tabCustomVars.putClientProperty("terminateEditOnFocusLost", true);
        tabCustomVars.getColumnModel().getColumn(0).setMinWidth(75);
        tabCustomVars.getColumnModel().getColumn(1).setMinWidth(100);
        tabCustomVars.setGridColor(Color.LIGHT_GRAY);
        JTableHeader tabMoreEqHeader = tabCustomVars.getTableHeader();
        tabMoreEqHeader.setPreferredSize(new Dimension(120, 20));
        JScrollPane tabMoreEqScrollPane = new JScrollPane(tabCustomVars);
        //tabMoreEqScrollPane.setMinimumSize(new Dimension(240,30));
 
        mapKeyFieldToValueField.put(keyCustomVars.toUpperCase(), 
                tabCustomVarsMod);
        
        tabMoreEqScrollPane.setAlignmentY(Component.TOP_ALIGNMENT);
 
        JButton btAtomSpecVar = new JButton("Add atom-specific variable");
        btAtomSpecVar.setToolTipText("Add the defintion of an atom specific variabnle.");
        btAtomSpecVar.addActionListener(new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e) {
                AtomSpecExpressionDefinition dialog = 
                        new AtomSpecExpressionDefinition(btAtomSpecVar);
                Object[] res = (Object[]) dialog.showDialog();
                if (res!=null)
                {
                    tabCustomVarsMod.addRow(res);
                }
            }
        });
        
        btnDDValueParams.addActionListener(new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e)
            {
                ParametrizedDescriptorDefinition dialog = 
                        new ParametrizedDescriptorDefinition(descNameToTune,
                                paramsToTune, btnDDValueParams);
                Object[] res = (Object[]) dialog.showDialog();
                if (res!=null)
                {
                    tabCustomVarsMod.addRow(res);
                }
            }
        });
        
        /*
        // Not active because it needs the definition of the descriptor and its parameters
        JButton btnParametrizedVar = new JButton("Add parametrized descriptor");
        btnParametrizedVar.setToolTipText("Defines a variable from a parametrized descriptor.");
        btnParametrizedVar.addActionListener(new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e) {
                ParametrizedDescriptorDefinition dialog = 
                        new ParametrizedDescriptorDefinition(descNameToTune,
                                paramsToTune);
                Object[] res = (Object[]) dialog.showDialog();
                if (res!=null)
                {
                    tabCustomVarsMod.addRow(res);
                }
            }
        });
        */
        
        JButton btnRemoveCustomVar = new JButton("Remove selected");
        btnRemoveCustomVar.setToolTipText("Remove the selected definitions.");
        btnRemoveCustomVar.addActionListener(new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e) {
                if (tabCustomVars.getRowCount() > 0)
                {
                    if (tabCustomVars.getSelectedRowCount() > 0)
                    {
                        int selectedRowIds[] = tabCustomVars.getSelectedRows();
                        Arrays.sort(selectedRowIds);
                        for (int i=(selectedRowIds.length-1); i>-1; i--)
                        {
                            tabCustomVarsMod.removeRow(selectedRowIds[i]);
                        }
                    }
                }
            }
        });
        
        GroupLayout lyoCustomvarPanel = new GroupLayout(lineCustomVars);
        lineCustomVars.setLayout(lyoCustomvarPanel);
        lyoCustomvarPanel.setAutoCreateGaps(true);
        lyoCustomvarPanel.setAutoCreateContainerGaps(true);
        lyoCustomvarPanel.setHorizontalGroup(
                lyoCustomvarPanel.createSequentialGroup()
                    .addComponent(tabMoreEqScrollPane)
                    .addGroup(lyoCustomvarPanel.createParallelGroup(
                            GroupLayout.Alignment.CENTER)
                        .addComponent(btAtomSpecVar)
                       // .addComponent(btnParametrizedVar)
                        .addComponent(btnRemoveCustomVar)));
        lyoCustomvarPanel.setVerticalGroup(
                lyoCustomvarPanel.createParallelGroup()
                    .addComponent(tabMoreEqScrollPane)
                    .addGroup(lyoCustomvarPanel.createSequentialGroup()
                        .addComponent(btAtomSpecVar)
                       // .addComponent(btnParametrizedVar)
                        .addComponent(btnRemoveCustomVar)));
        
        localBlock4.add(lineCustomVars);
        
 
        //HEREGOESADVIMPLEMENTATION this is only to facilitate automated insertion of code       
        
        // From here it's all about advanced options
        /*
        JPanel advOptsBlock = new JPanel();
        advOptsBlock.setVisible(false);
        advOptsBlock.setLayout(new BoxLayout(advOptsBlock, SwingConstants.VERTICAL));
 
        */
        
        /*
        JButton advOptShow = new JButton("Advanced Settings");
        advOptShow.addActionListener(new ActionListener(){
            public void actionPerformed(ActionEvent e){
                if (advOptsBlock.isVisible())
                {
                    advOptsBlock.setVisible(false);
                    advOptShow.setText("Show Advanced Settings");                   
                }
                else
                {
                    advOptsBlock.setVisible(true);
                    advOptShow.setText("Hide Advanced Settings");
                    scrollablePane.validate();
                    scrollablePane.repaint();
                    scrollablePane.getVerticalScrollBar().setValue(
                            scrollablePane.getVerticalScrollBar().getValue() + (int) preferredHeight*2/3);
                }
            }
        });
        
        JPanel advOptsController = new JPanel();
        advOptsController.setPreferredSize(fileLabelSize); 
        advOptsController.add(advOptShow);
        block.add(new JSeparator());
        block.add(advOptsController);
        block.add(advOptsBlock);  
        */
        
        block.add(super.getPanelForUnformattedInput());
        
        this.add(scrollablePane);
    }
    
//------------------------------------------------------------------------------
    
    protected void setVisibilityAccordingToFitnessProviderSelection() 
    {
        if (rdbIntOrExt.isSelected())
        {
            localBlock3.setVisible(true);
            localBlock4.setVisible(false);
        }
        else
        {
            localBlock3.setVisible(false);
            localBlock4.setVisible(true);
        }
    }
    
//------------------------------------------------------------------------------
    
    @Override
    protected void preliminatyTasksUponImportingParams()
    {
        int initialRowCount = tabCustomVarsMod.getRowCount();
        for (int i=0; i<initialRowCount; i++)
        {
            tabCustomVarsMod.removeRow(0);
        }
    }
    
//------------------------------------------------------------------------------
    
    @Override
    protected void adaptVisibility() 
    {
        setVisibilityAccordingToFitnessProviderSelection();
    }
 
//------------------------------------------------------------------------------
    
    @SuppressWarnings("serial")
    private class DescriptorTreeNode extends DefaultMutableTreeNode
    {
        protected DescriptorForFitness dff;
 
        public DescriptorTreeNode(DescriptorForFitness dff) {
            super(dff.getShortName());
            this.dff = dff;
        }
 
        public DescriptorTreeNode(String descriptorName, DescriptorForFitness dff) {
            super(descriptorName);
            this.dff = dff;
        }
 
        public DescriptorTreeNode(String kls) {
            super(kls);
        }
    }
    
//-----------------------------------------------------------------------------
    
    @Override
    public void importParametersFromDenoptimParamsFile(String fileName) throws Exception
    {
        clearUnformattedTxtArea();
        importParametersFromDenoptimParamsFile(fileName,"FP-");
        
        rdbSrcOrNew.setSelected(false);
        localBlock1.setVisible(false);
        localBlock2.setVisible(true);       
        if (rdbIntOrExt.isSelected())
        {
            localBlock3.setVisible(true);
            localBlock4.setVisible(false);
        }
        else
        {
            localBlock3.setVisible(false);
            localBlock4.setVisible(true);
        }
        showUnknownKeyWarning(this, "Fitness Provider");
    }
 
//-----------------------------------------------------------------------------
    
    @SuppressWarnings("unchecked")
    @Override
    public void importSingleParameter(String key, String value) throws Exception 
    {
        Object valueField;
        String valueFieldClass;
        if (mapKeyFieldToValueField.containsKey(key.toUpperCase()))
        {
            valueField = mapKeyFieldToValueField.get(key.toUpperCase());
            valueFieldClass = valueField.getClass().toString();
        }
        else
        {
            addToUnformattedTxt(key, value);
            return;
        }
        
        switch (valueFieldClass)
        {
            case "class javax.swing.JTextField":
                if (key.toUpperCase().equals(keyFitProviderSource.toUpperCase())) 
                {
                    rdbIntOrExt.setSelected(true);
                }
                if (key.toUpperCase().equals(keyEq.toUpperCase()))
                {
                    value = value.trim();
                    if (value.startsWith("${") && value.endsWith("}"));
                    {
                        value = value.substring(2, value.lastIndexOf("}"));
                    }
                }
                ((JTextField) valueField).setText(value);
                break;
                
            case "class javax.swing.JRadioButton":
                if (key.toUpperCase().equals(key3dTrees.toUpperCase()))
                {
                    ((JRadioButton) valueField).setSelected(false);
                } else {
                    ((JRadioButton) valueField).setSelected(true);
                }
                
                if (key.toUpperCase().equals(keyPreFitnessUIDCheck.toUpperCase()))
                {
                   ((JRadioButton) valueField).setSelected(
                           RunTimeParameters.readYesNoTrueFalse(value));
                }
                break;
                
            case "class javax.swing.JComboBox":
                ((JComboBox<String>) valueField).setSelectedItem(value);
                break;
                
            case "class javax.swing.table.DefaultTableModel":
                if (key.toUpperCase().equals(keyCustomVars.toUpperCase())) 
                {
                    String noHead = value.replace("${atomSpecific('", "");
                    Object[] rowContent = new Object[2];
                    rowContent[0] = noHead.split("'")[0];
                    rowContent[1] = value;
                    ((DefaultTableModel) valueField).addRow(rowContent);
                } else {
                    //WARNING: there might be other cases where we do not take 
                    // all the row/columns
                    ((DefaultTableModel) valueField).addRow(value.split(" "));
                }
                break;
                
            default:
                throw new Exception("<html>Unexpected type for parameter: "  
                        + key + " (" + valueFieldClass 
                        + ").<br>Please report this to"
                        + "the DEMOPTIM team.</html>");
        }
    }
    
//-----------------------------------------------------------------------------
    
    @Override
    public void putParametersToString(StringBuilder sb) throws Exception
    {
        sb.append(NL);
        sb.append("# Fitness Provider - parameters").append(NL);
        if (rdbIntOrExt.isSelected())
        {
            sb.append(getStringIfNotEmpty(keyFitProviderSource,
                    txtFitProviderSource));
            sb.append(keyFitProviderInterpreter).append("=").append(
                    txtFitProviderInterpreter.getText()).append(NL);
        } else {
            sb.append(getStringIfNotEmpty(keyEq,txtEq,"${","}"));
            for (int i=0; i<tabCustomVarsMod.getRowCount(); i++) 
            {
                sb.append(keyCustomVars).append("=").append(
                        tabCustomVarsMod.getValueAt(i, 1)).append(NL);
            }
        }
        if (!rdb3dTrees.isSelected())
        {
            sb.append(key3dTrees).append(NL);
        }
        if (rdbPreFitnessUIDCheck.isSelected())
        {
            sb.append(keyPreFitnessUIDCheck).append("=YES").append(NL);
        } else {
            sb.append(keyPreFitnessUIDCheck).append("=NO").append(NL);
        }
        
        sb.append(getTextForUnformattedSettings()).append(NL);
        
        //HEREGOESPRINT this is only to facilitate automated insertion of code       
    }
    
//------------------------------------------------------------------------------
    
    @SuppressWarnings("serial")
    private class ParametrizedDescriptorDefinition extends GUIModalDialog
    {   
        public ParametrizedDescriptorDefinition(String descName, 
                String[] paramNames, Component refForPlacement)
        {
            super(refForPlacement, true);
            this.setTitle("Define parametrized descriptor variable");
            
            Dimension sizeNameFields = new Dimension(200,preferredHeight);
            Dimension sizeNameLbls = new Dimension(120,preferredHeight);
            
            JPanel rowOne = new JPanel(new FlowLayout(FlowLayout.LEFT));
            JLabel lblVarName = new JLabel("Variable name: ");
            lblVarName.setPreferredSize(sizeNameLbls);
            lblVarName.setToolTipText("<html>This is the string representing "
                    + "a user-defined variable <br> in the expression of the "
                    + "fitness.</html>");
            JTextField txtVarName = new JTextField();
            txtVarName.setPreferredSize(sizeNameFields);
            rowOne.add(lblVarName);
            rowOne.add(txtVarName);
            
            JPanel rowTwo = new JPanel(new FlowLayout(FlowLayout.LEFT));
            JLabel lblDescName = new JLabel("Descriptor name: ");
            lblDescName.setPreferredSize(sizeNameLbls);
            lblDescName.setToolTipText("<html>This is the pre-defined short "
                    + "name "
                    + "reported <br>in "
                    + "the collection of descriptors.</html>");
            JTextField txtDescName = new JTextField(descName);
            txtDescName.setPreferredSize(sizeNameFields);
            rowTwo.add(lblDescName);
            rowTwo.add(txtDescName);
            
            JPanel rowThree = new JPanel();
            rowThree.setLayout(new BorderLayout());
            JLabel lblParams = new JLabel("Parameters:");
            String paramToolTip = "<html>The parameters provided in the "
                    + "order defined in the description <br> "
                    + "of the descriptor. Only the parameter value is needed, "
                    + "not its name.</html>";
            lblParams.setToolTipText(paramToolTip);
            
            JTable tabParams;
            DefaultTableModel tabParamsMod = new DefaultTableModel();
            tabParamsMod.setColumnCount(1);
            int tabSize = paramNames.length;
            tabParamsMod.setRowCount(tabSize);
            tabParams = new JTable(tabParamsMod);
            tabParams.setToolTipText(paramToolTip);
            tabParams.putClientProperty("terminateEditOnFocusLost", true);
            tabParams.getColumnModel().getColumn(0).setMinWidth(150);
            tabParams.setGridColor(Color.LIGHT_GRAY);
            JScrollPane txtParamScrollPane = new JScrollPane(tabParams);
            tabParams.setTableHeader(null);
            
            rowThree.add(lblParams,BorderLayout.WEST);
            rowThree.add(txtParamScrollPane,BorderLayout.CENTER);
            JPanel firstTwo = new JPanel();
            firstTwo.setLayout(new BoxLayout(firstTwo, 
                    SwingConstants.VERTICAL));
            firstTwo.add(rowOne);
            firstTwo.add(rowTwo);
            addToNorthPane(firstTwo);
            addToCentralPane(rowThree);
            this.btnDone.addActionListener(new ActionListener() {
                @Override
                public void actionPerformed(ActionEvent e) {
                    if (txtVarName.getText().equals("")
                            || txtDescName.getText().equals(""))
                    {
                        result = null;
                    } else {
                        String line = "${Variable.parametrized('" 
                    + txtVarName.getText() 
                                + "','" + txtDescName.getText() + "','";
                        // First check that all parameters were given
                        boolean quit = false;
                        for (int i=0; i<tabSize; i++)
                        {
                            if (tabParamsMod.getValueAt(i,0) == null || 
                                    tabParamsMod.getValueAt(i,0).toString().trim().equals(""))
                                quit = true;
                        }
                        
                        if (!quit)
                        {
                            //NB: all params are collected into a single string!
                            for (int i=0; i<tabSize; i++)
                            {   
                                String s = tabParamsMod.getValueAt(i,0).toString()
                                        .trim();
                                if (s.contains(paramNames[i]))
                                {
                                    s = s.replaceFirst(paramNames[i],"");
                                    s = s.trim();
                                    if (s.startsWith("="))
                                    {
                                        s = s.replaceFirst("=","");
                                        s = s.trim();
                                    }
                                }
                                line = line + s;
                                if (i<(tabSize-1))
                                    line = line  + ", ";
                            }
                            line = line + "')}";
                            result = new Object[] {txtVarName.getText(),line};
                        }
                    }
                    close();
                }
            });
            this.btnExtra.setText("?");
            this.btnExtra.setVisible(true);
            this.btnExtra.addActionListener(new ActionListener() {
                @Override
                public void actionPerformed(ActionEvent e) {
                    String txt = "<html><body width='%1s'>"
                        + "Here you can define:<ul>"
                        + "<li>the name of the variable, i.e., "
                        + "the string used to represent this variable in the "
                        + "equation defining the fitness,</li>"
                        + "<li>the name of the descriptor this variable is "
                        + "based on, i.e., the unique string identifying the "
                        + "descriptor in the list of available descriptors,</li>"
                        + "<li>the list of parameters that customize the "
                        + "calculation of the descriptor. The values of the "
                        + "parameters should be given in the order specified in "
                        + "the description of the descriptor.</li>"
                        + "</ul></html>";
                JOptionPane.showMessageDialog(btnExtra, 
                        String.format(txt, 350),
                        "Tips",
                        JOptionPane.PLAIN_MESSAGE);
                }
            });
            
            this.btnCanc.addActionListener(new ActionListener() {
                @Override
                public void actionPerformed(ActionEvent e) {
                    result = null;
                    close();
                }
            });
        }
    }
    
//------------------------------------------------------------------------------
    
    @SuppressWarnings("serial")
    private class AtomSpecExpressionDefinition extends GUIModalDialog
    {
        public AtomSpecExpressionDefinition(Component refForPlacement)
        {
            super(refForPlacement);
            this.setTitle("Define atom-specific variable");
            
            Dimension sizeNameFields = new Dimension(200,preferredHeight);
            Dimension sizeNameLbls = new Dimension(120,preferredHeight);
            
            JPanel rowOne = new JPanel(new FlowLayout(FlowLayout.LEFT));
            JLabel lblVarName = new JLabel("Variable name: ");
            lblVarName.setPreferredSize(sizeNameLbls);
            lblVarName.setToolTipText("<html>This is the string representing "
                    + "a user-defined variable <br> in the expression of the "
                    + "fitness.</html>");
            JTextField txtVarName = new JTextField();
            txtVarName.setPreferredSize(sizeNameFields);
            rowOne.add(lblVarName);
            rowOne.add(txtVarName);
            
            JPanel rowTwo = new JPanel(new FlowLayout(FlowLayout.LEFT));
            JLabel lblDescName = new JLabel("Descriptor name: ");
            lblDescName.setPreferredSize(sizeNameLbls);
            lblDescName.setToolTipText("<html>This is the pre-defined short "
                    + "name "
                    + "reported <br>in "
                    + "the collection of descriptors.</html>");
            JTextField txtDescName = new JTextField();
            txtDescName.setPreferredSize(sizeNameFields);
            rowTwo.add(lblDescName);
            rowTwo.add(txtDescName);
            
            JPanel rowThree = new JPanel();
            rowThree.setLayout(new BorderLayout());
            JLabel lblSmarts = new JLabel("SMARTS:");
            lblSmarts.setToolTipText("<html>The SMARTS query used to identify "
                    + "specific atom/bonds to <br> "
                    + "be used for the calculation of "
                    + "the numerical value of this variable.</html>");
            JEditorPane txtSmarts = new JEditorPane();
            JScrollPane txtSmartsScrollPane = new JScrollPane(txtSmarts);
            rowThree.add(lblSmarts,BorderLayout.WEST);
            rowThree.add(txtSmartsScrollPane,BorderLayout.CENTER);
            JPanel firstTwo = new JPanel();
            firstTwo.setLayout(new BoxLayout(firstTwo, 
                    SwingConstants.VERTICAL));
            firstTwo.add(rowOne);
            firstTwo.add(rowTwo);
            addToNorthPane(firstTwo);
            addToCentralPane(rowThree);
            this.btnDone.addActionListener(new ActionListener() {
                
                @Override
                public void actionPerformed(ActionEvent e) {
                    if (txtVarName.getText().equals("")
                            && txtDescName.getText().equals("")
                            && txtSmarts.getText().equals(""))
                    {
                        result = null;
                    } else {
                        result = new Object[] {txtVarName.getText(), 
                                "${atomSpecific('" + txtVarName.getText() 
                                + "','" + txtDescName.getText() + "','"
                                + txtSmarts.getText() + "')}"};
                    }
                    close();
                }
            });
            this.btnCanc.addActionListener(new ActionListener() {
                
                @Override
                public void actionPerformed(ActionEvent e) {
                    result = null;
                    close();
                }
            });
        }
    }
}