GAParametersForm.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.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.atomic.AtomicInteger;
 
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.GroupLayout;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
import javax.swing.JSpinner;
import javax.swing.JTextField;
import javax.swing.SpinnerNumberModel;
import javax.swing.SwingConstants;
import javax.swing.UIManager;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
import javax.swing.table.DefaultTableModel;
 
import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
import org.jfree.data.xy.DefaultXYDataset;
 
import denoptim.ga.EAUtils;
import denoptim.programs.denovo.GAParameters;
 
 
public class GAParametersForm extends ParametersForm
{
 
    private static final long serialVersionUID = 5067352357196631445L;
    
    public static AtomicInteger gaFormUID = new AtomicInteger(1);
    
    private Map<String,Object> mapKeyFieldToValueField;
    
    JPanel block;    
    JPanel localBlock1;
    JPanel localBlock2;
    JPanel advOptsBlock;
    
    JPanel lineSrcOrNew;
    JRadioButton rdbSrcOrNew;
    
    JPanel lineGASource;
    JLabel lblGASource;
    JTextField txtGASource;
    JButton btnGASource;
    JButton btnLoadGASource;
    
    String keyPar3 = "GA-RandomSeed";
    JPanel linePar3;
    JLabel lblPar3;
    JTextField txtPar3;
 
    String keyPar1 = "GA-PrecisionLevel";
    JPanel linePar1;
    JLabel lblPar1;
    JTextField txtPar1;
 
    String keyPar2 = "GA-Verbosity";
    JPanel linePar2;
    JLabel lblPar2;
    JComboBox<String> cmbPar2;
 
    String keyPar5 = "GA-SortByIncreasingFitness";
    JPanel linePar5;
    JRadioButton rdbPar5;
 
    String keyPar5a = "GA-NaNFitnessKillsExperiment";
    JPanel linePar5a;
    JRadioButton rdbPar5a;
 
    String keyPar6 = "GA-PopulationSize";
    JPanel linePar6;
    JLabel lblPar6;
    JTextField txtPar6;
 
    String keyPar7 = "GA-NumChildren";
    JPanel linePar7;
    JLabel lblPar7;
    JTextField txtPar7;
 
    String keyPar8 = "GA-NumGenerations";
    JPanel linePar8;
    JLabel lblPar8;
    JTextField txtPar8;
 
    String keyPar9 = "GA-NumConvGen";
    JPanel linePar9;
    JLabel lblPar9;
    JTextField txtPar9;
 
    String keyPar10 = "GA-MaxTriesPerPopulation";
    JPanel linePar10;
    JLabel lblPar10;
    JTextField txtPar10;
    
    JPanel lineMolToGraph;
    JLabel lblMolToGraph;
    JTextField txtMolToGraph;
    JButton btnMolToGraph;
    String keyMolToGraph = "GA-InitMolsToFragmentFile";
    
    JPanel lineFrgMols;
    JLabel lblFrgMols;
    JTextField txtFrgMols;
    JButton btnFrgMols;
    String keyFrgMols = "FRG-CuttingRulesFile";
    
    JPanel lineAddH;
    JLabel lblAddH;
    JRadioButton rdbAddH;
    String keyAddH = "FRG-AddExplicitHydrogen";
    
    JPanel lineGrowthPropMode;
    JLabel lblGrowthPropMode;
    ButtonGroup bgGrowthMode;
    JRadioButton rbtLevelGrowth;
    JRadioButton rbtMolSzGrowth;
    
    DefaultXYDataset molSizeProbData;
    JFreeChart graphMolSzProbJFChart;
    JPanel graphMolSzProbJFChartChartPanel;
    JPanel graphMolSzProbJFChartCtrlPanel;
    JPanel graphMolSzProbSpinnerPane;
    Double minMolSizeProbPlot = 1.0;
    Double maxMolSizeProbPlot = 50.0;
 
    String keyParMolSz1 = "GA-MolGrowthProbScheme";
    JPanel lineParMolSz1;
    JLabel lblParMolSz1;
    JComboBox<ProbabilityFuncitonShape> cmbParMolSz1;
 
    String keyParMolSz2 = "GA-MolGrowthMultiplier";
    JPanel lineParMolSz2;
    JLabel lblParMolSz2;
    JSpinner spnParMolSz2;
 
    String keyParMolSz3 = "GA-MolGrowthSigmaSteepness";
    JPanel lineParMolSz3;
    JLabel lblParMolSz3;
    JSpinner spnParMolSz3;
 
    String keyParMolSz4 = "GA-MolGrowthSigmaMiddle";
    JPanel lineParMolSz4;
    JLabel lblParMolSz4;
    JSpinner spnParMolSz4;
    
    JPanel localBlockMolSz3;
    JPanel localBlockMolSz4;
    JPanel localBlockMolSzGraph;
    JPanel localBlockMolSzAll;
    
    DefaultXYDataset levelProbData;
    JFreeChart graphLvlProbJFChart;
    JPanel graphLvlProbJFChartChartPanel;
    JPanel graphLvlProbJFChartCtrlPanel;
    JPanel graphLvlProbSpinnerPane;
    Double minLevelProbPlot = 0.0;
    Double maxLevelProbPlot = 5.0;
 
    String keyPar11 = "GA-LevelGrowthProbScheme";
    JPanel linePar11;
    JLabel lblPar11;
    JComboBox<ProbabilityFuncitonShape> cmbPar11;
 
    String keyPar12 = "GA-LevelGrowthMultiplier";
    JPanel linePar12;
    JLabel lblPar12;
    JSpinner spnPar12;
 
    String keyPar13 = "GA-LevelGrowthSigmaSteepness";
    JPanel linePar13;
    JLabel lblPar13;
    JSpinner spnPar13;
 
    String keyPar14 = "GA-LevelGrowthSigmaMiddle";
    JPanel linePar14;
    JLabel lblPar14;
    JSpinner spnPar14;
    
    JPanel localBlockLvlProb3;
    JPanel localBlockLvlProb4;
    JPanel localBlockLvlProbGraph;
    JPanel localBlockLvlProbAll;
    
    DefaultXYDataset crowdProbData;
    JFreeChart graphCrowdProbJFChart;
    JPanel graphCrowdProbJFChartChartPanel;
    JPanel graphCrowdProbJFChartCtrlPanel;
    JPanel graphCrowdProbSpinnerPane;
    Double minLevelCrowdProbPlot = 0.0;
    Double maxLevelCrowdProbPlot = 6.0;
    
    JPanel localBlockCrowd3;
    JPanel localBlockCrowd4;
    JPanel localBlockCrowdGraph;
 
    String keyParCrowd1 = "GA-CrowdProbScheme";
    JPanel lineParCrowd1;
    JLabel lblParCrowd1;
    JComboBox<ProbabilityFuncitonShape> cmbParCrowd1;
 
    String keyParCrowd2 = "GA-CrowdMultiplier";
    JPanel lineParCrowd2;
    JLabel lblParCrowd2;
    JSpinner spnParCrowd2;
 
    String keyParCrowd3 = "GA-CrowdSigmaSteepness";
    JPanel lineParCrowd3;
    JLabel lblParCrowd3;
    JSpinner spnParCrowd3;
 
    String keyParCrowd4 = "GA-CrowdSigmaMiddle";
    JPanel lineParCrowd4;
    JLabel lblParCrowd4;
    JSpinner spnParCrowd4;
 
    String keyPar15 = "GA-XOverSelectionMode";
    JPanel linePar15;
    JLabel lblPar15;
    JComboBox<String> cmbPar15;
 
    String keyPar16 = "GA-CrossoverWeight";
    JPanel linePar16;
    JLabel lblPar16;
    JTextField txtPar16;
 
    String keyPar17 = "GA-MutationWeight";
    JPanel linePar17;
    JLabel lblPar17;
    JTextField txtPar17;
    
    String keyParMSM = "GA-MultiSiteMutationWeights";
    JPanel lineParMSM;
    JLabel lblParMSM;
    JTextField txtParMSM;
    
    String keyParWC = "GA-ConstructionWeight";
    JPanel lineParWC;
    JLabel lblParWC;
    JTextField txtParWC;
 
    String keyPar18 = "GA-SymmetryProbability";
    JPanel linePar18;
    JLabel lblPar18;
    JTextField txtPar18;
 
    String keyPar19 = "GA-ReplacementStrategy";
    JPanel linePar19;
    JLabel lblPar19;
    JComboBox<String> cmbPar19;
 
    String keyPar20 = "GA-InitPoplnFile";
    JPanel linePar20;
    JLabel lblPar20;
    JTextField txtPar20;
    JButton btnPar20;
 
    String keyPar21 = "GA-UIDFileIn";
    JPanel linePar21;
    JLabel lblPar21;
    JTextField txtPar21;
    JButton btnPar21;
 
    String keyPar22 = "GA-UIDFileOut";
    JPanel linePar22;
    JLabel lblPar22;
    JTextField txtPar22;
    JButton btnPar22;
 
    String keyPar24 = "GA-NumParallelTasks";
    JPanel linePar24;
    JLabel lblPar24;
    JTextField txtPar24;
 
    String keyPar25 = "GA-Parallelization";
    JPanel linePar25;
    JLabel lblPar25;
    JComboBox<String> cmbPar25;
    
    String keyRingTmplsFrags = "GA-KeepNewRingSystemVertexes";
    JPanel lineRingTmplsFrags;
    JRadioButton rdbRingTmplsFrags;
    
    String keyRingTmplsScaff = "GA-KeepNewRingSystemScaffolds";
    JPanel lineRingTmplsScaff;
    JRadioButton rdbRingTmplsScaff;
    
    String keyRingSysTmplTrhld = "GA-KeepNewRingSystemFitnessTrsh";
    JPanel lineRingSysTmpl;
    JLabel lblRingSysTmpl;
    JSpinner spnRingSysTmpl;
    
    public enum ProbabilityFuncitonShape {EXP_DIFF, TANH, 
            SIGMA, UNRESTRICTED};
 
    //HEREGOFIELDS  this is only to facilitate automated insertion of code
 
    
    String NL = System.getProperty("line.separator");
    
    public GAParametersForm(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));
        
        localBlockMolSz3 = new JPanel();
        localBlockMolSz3.setVisible(false);
        localBlockMolSz3.setLayout(new BoxLayout(localBlockMolSz3, 
                SwingConstants.VERTICAL));
 
        localBlockMolSz4 = new JPanel();
        localBlockMolSz4.setVisible(true);
        localBlockMolSz4.setLayout(new BoxLayout(localBlockMolSz4, 
                SwingConstants.VERTICAL));
 
        localBlockMolSzGraph = new JPanel();
        localBlockMolSzGraph.setVisible(true);
        localBlockMolSzAll = new JPanel();
        localBlockMolSzAll.setVisible(false);
        localBlockMolSzAll.setLayout(new BoxLayout(localBlockMolSzAll, 
                SwingConstants.VERTICAL));
        
        localBlockLvlProb3 = new JPanel();
        localBlockLvlProb3.setVisible(true);
        localBlockLvlProb3.setLayout(new BoxLayout(localBlockLvlProb3, 
                SwingConstants.VERTICAL));
        
        localBlockLvlProb4 = new JPanel();
        localBlockLvlProb4.setVisible(false);
        localBlockLvlProb4.setLayout(new BoxLayout(localBlockLvlProb4, 
                SwingConstants.VERTICAL));
        
        localBlockLvlProbGraph = new JPanel();
        localBlockLvlProbGraph.setVisible(true);
        localBlockLvlProbAll = new JPanel();
        localBlockLvlProbAll.setVisible(true);
        localBlockLvlProbAll.setLayout(new BoxLayout(localBlockLvlProbAll, 
                SwingConstants.VERTICAL));
        
        localBlockCrowd3 = new JPanel();
        localBlockCrowd3.setVisible(false);
        localBlockCrowd3.setLayout(new BoxLayout(localBlockCrowd3, 
                SwingConstants.VERTICAL));
        
        localBlockCrowd4 = new JPanel();
        localBlockCrowd4.setVisible(false);
        localBlockCrowd4.setLayout(new BoxLayout(localBlockCrowd4, 
                SwingConstants.VERTICAL));
        
        localBlockCrowdGraph = new JPanel();
        localBlockCrowdGraph.setVisible(false);
        
        advOptsBlock = new JPanel();
        advOptsBlock.setVisible(false);
        advOptsBlock.setLayout(new BoxLayout(advOptsBlock, 
                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 toolTipGASource = "<html>Pathname of a DENOPTIM's parameter file with GA settings.</html>";
        lineGASource = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblGASource = new JLabel("Use parameters from file:", SwingConstants.LEFT);
        lblGASource.setToolTipText(toolTipGASource);
        txtGASource = new JTextField();
        txtGASource.setToolTipText(toolTipGASource);
        txtGASource.setPreferredSize(fileFieldSize);
        btnGASource = new JButton("Browse");
        btnGASource.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
                GUIFileOpener.pickFileForTxtField(txtGASource,
                        btnGASource);
           }
        });
        btnLoadGASource = new JButton("Load...");
        txtGASource.setToolTipText("<html>Specify the file containing the "
                + "parameters to be loaded in this form.</html>");
        btnLoadGASource.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                try 
                {
                    importParametersFromDenoptimParamsFile(txtGASource.getText());
                } 
                catch (Exception e1) 
                {
                    if (e1.getMessage().equals("") || e1.getMessage() == null)
                    {
                        e1.printStackTrace();
                        JOptionPane.showMessageDialog(btnLoadGASource,
                                "<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(btnLoadGASource,
                                e1.getMessage(),
                                "Error",
                                JOptionPane.ERROR_MESSAGE,
                                UIManager.getIcon("OptionPane.errorIcon"));
                    }
                    return;
                }
            }
        });
        lineGASource.add(lblGASource);
        lineGASource.add(txtGASource);
        lineGASource.add(btnGASource);
        lineGASource.add(btnLoadGASource);
        localBlock1.add(lineGASource);
        
        //HEREGOESIMPLEMENTATION this is only to facilitate automated insertion of code
 
        String toolTipPar6 = "Specifies the number of individuals in the population.";
        linePar6 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar6 = new JLabel("Size of population:", SwingConstants.LEFT);
        lblPar6.setPreferredSize(fileLabelSize);
        lblPar6.setToolTipText(toolTipPar6);
        txtPar6 = new JTextField();
        txtPar6.setToolTipText(toolTipPar6);
        txtPar6.setPreferredSize(strFieldSize);
        txtPar6.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar6.toUpperCase(),txtPar6);
        linePar6.add(lblPar6);
        linePar6.add(txtPar6);
        localBlock2.add(linePar6);
        
        String toolTipPar7 = "Specifies the number of children to be generated for each generation.";
        linePar7 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar7 = new JLabel("No. offsprings per generation:", SwingConstants.LEFT);
        lblPar7.setPreferredSize(fileLabelSize);
        lblPar7.setToolTipText(toolTipPar7);
        txtPar7 = new JTextField();
        txtPar7.setToolTipText(toolTipPar7);
        txtPar7.setPreferredSize(strFieldSize);
        txtPar7.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar7.toUpperCase(),txtPar7);
        linePar7.add(lblPar7);
        linePar7.add(txtPar7);
        localBlock2.add(linePar7);
 
        String toolTipPar8 = "Specifies the maximum number of generation.";
        linePar8 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar8 = new JLabel("Max. number of generations:", SwingConstants.LEFT);
        lblPar8.setPreferredSize(fileLabelSize);
        lblPar8.setToolTipText(toolTipPar8);
        txtPar8 = new JTextField();
        txtPar8.setToolTipText(toolTipPar8);
        txtPar8.setPreferredSize(strFieldSize);
        txtPar8.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar8.toUpperCase(),txtPar8);
        linePar8.add(lblPar8);
        linePar8.add(txtPar8);
        localBlock2.add(linePar8);
 
        String toolTipPar9 = "Specifies the convergence criterion as number of subsequent identical generations.";
        linePar9 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar9 = new JLabel("Max. stagnating generations:", SwingConstants.LEFT);
        lblPar9.setPreferredSize(fileLabelSize);
        lblPar9.setToolTipText(toolTipPar9);
        txtPar9 = new JTextField();
        txtPar9.setToolTipText(toolTipPar9);
        txtPar9.setPreferredSize(strFieldSize);
        txtPar9.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar9.toUpperCase(),txtPar9);
        linePar9.add(lblPar9);
        linePar9.add(txtPar9);
        localBlock2.add(linePar9);
        
        localBlock2.add(new JSeparator());
        
        lineGrowthPropMode = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblGrowthPropMode = new JLabel("Graph growth controlled by: ");
        bgGrowthMode = new ButtonGroup();
        rbtLevelGrowth = new JRadioButton("graph deepness (level)");
        rbtLevelGrowth.setSelected(true);
        rbtLevelGrowth.addActionListener(new ActionListener(){
            public void actionPerformed(ActionEvent e){
                if (rbtLevelGrowth.isSelected())
                {
                    localBlockLvlProbAll.setVisible(true);
                    localBlockMolSzAll.setVisible(false);
                }
            }
        });
        rbtLevelGrowth.addChangeListener(rdbFieldChange);
        rbtMolSzGrowth = new JRadioButton("molecular size (heavy atoms count)");
        rbtMolSzGrowth.addActionListener(new ActionListener(){
            public void actionPerformed(ActionEvent e){
                if (rbtMolSzGrowth.isSelected())
                {
                    localBlockLvlProbAll.setVisible(false);
                    localBlockMolSzAll.setVisible(true);
                }
            }
        });
        rbtMolSzGrowth.addChangeListener(rdbFieldChange);
        bgGrowthMode.add(rbtLevelGrowth);
        bgGrowthMode.add(rbtMolSzGrowth);
        lineGrowthPropMode.add(lblGrowthPropMode);
        lineGrowthPropMode.add(rbtLevelGrowth);
        lineGrowthPropMode.add(rbtMolSzGrowth);
        localBlock2.add(lineGrowthPropMode);
        
        String toolTipPar12 = "<html>Specifies the value of the factor used in"
                + " growth probability schemes <code>"
                + ProbabilityFuncitonShape.EXP_DIFF + "</code> and "
                + "<code>"
                + ProbabilityFuncitonShape.TANH + "</code></html>";
        linePar12 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar12 = new JLabel("<html>Graph growth by level - parameter "
                + "<code>&lambda;</code><html>", SwingConstants.LEFT);
        lblPar12.setPreferredSize(fileLabelSize);
        lblPar12.setToolTipText(toolTipPar12);
        spnPar12 = new JSpinner(new SpinnerNumberModel(1.0, 0.0, null, 0.1));
        spnPar12.setToolTipText(toolTipPar12);
        spnPar12.setPreferredSize(strFieldSize);
        mapKeyFieldToValueField.put(keyPar12.toUpperCase(),spnPar12);
        linePar12.add(lblPar12);
        linePar12.add(spnPar12);
        localBlockLvlProb3.add(linePar12);
        
        String toolTipPar13 = "<html>Specifies the value of parameter "
                + "&sigma;<sub>1</sub> used for growth probability scheme"
                + " <code>"
                + ProbabilityFuncitonShape.SIGMA
                + "</code>.<br>It corresponds to the steepness of"
                + " the function where <i>P(level) = 50%</i></html>";
        linePar13 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar13 = new JLabel("<html>Graph growth by level - parameter "
                + "<code>&sigma;</code><sub>1</sub>:</html>", 
                SwingConstants.LEFT);
        lblPar13.setPreferredSize(fileLabelSize);
        lblPar13.setToolTipText(toolTipPar13);
        spnPar13 = new JSpinner(new SpinnerNumberModel(1.0, null, null, 0.1));
        spnPar13.setToolTipText(toolTipPar13);
        spnPar13.setPreferredSize(strFieldSize);
        mapKeyFieldToValueField.put(keyPar13.toUpperCase(),spnPar13);
        linePar13.add(lblPar13);
        linePar13.add(spnPar13);
        localBlockLvlProb4.add(linePar13);
        
        String toolTipPar14 = "<html>Specifies the value of parameter "
                + "&sigma;<sub>2</sub> used in growth probability scheme "
                + "<code>"
                + ProbabilityFuncitonShape.SIGMA
                + "</code>.<br>It corresponds to the level "
                + "where <i>P(level) = 50%</i></html>";
        linePar14 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar14 = new JLabel("<html>Graph growth by level - parameter "
                + "<code>&sigma;</code><sub>2</sub>:<html>", 
                SwingConstants.LEFT);
        lblPar14.setPreferredSize(fileLabelSize);
        lblPar14.setToolTipText(toolTipPar14);
        spnPar14 = new JSpinner(new SpinnerNumberModel(3.5, null, null, 0.1));
        spnPar14.setToolTipText(toolTipPar14);
        spnPar14.setPreferredSize(strFieldSize);
        mapKeyFieldToValueField.put(keyPar14.toUpperCase(),spnPar14);
        linePar14.add(lblPar14);
        linePar14.add(spnPar14);
        localBlockLvlProb4.add(linePar14);
        
        String toolTipPar11 = "Specifies the growth probability scheme";
        linePar11 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar11 = new JLabel("Graph extension probability function:", 
                SwingConstants.LEFT);
        lblPar11.setPreferredSize(fileLabelSize);
        lblPar11.setToolTipText(toolTipPar11);
        cmbPar11 = new JComboBox<ProbabilityFuncitonShape>(
                ProbabilityFuncitonShape.values());
        cmbPar11.setSelectedItem(ProbabilityFuncitonShape.EXP_DIFF);
        cmbPar11.setToolTipText(toolTipPar11);
        cmbPar11.addActionListener(cmbFieldChange);
        mapKeyFieldToValueField.put(keyPar11.toUpperCase(),cmbPar11);
        
        // NB: we need to create the graph before setting the action listeners
        //     that will eventually edit the data plotted.
        createLvlProbGraph();
        
        graphLvlProbJFChartCtrlPanel = new JPanel(new BorderLayout());
        graphLvlProbJFChartCtrlPanel.setMaximumSize(new Dimension(100,100));
        graphLvlProbSpinnerPane = new JPanel(new GridLayout(0,2));
        final JSpinner spnMaxLev = new JSpinner(new SpinnerNumberModel(
                maxLevelProbPlot.intValue(), 1, null, 1));
        spnMaxLev.addChangeListener(new ChangeListener()
        {
            @Override
            public void stateChanged(ChangeEvent event)
            {
                int maxLev = ((Integer) spnMaxLev.getValue()).intValue();                
                ((XYPlot) graphLvlProbJFChart.getPlot())
                    .getDomainAxis().setRange(minLevelProbPlot, maxLev);
            }
        }); 
        graphLvlProbSpinnerPane.add(new JLabel("X-axis max: "));
        graphLvlProbSpinnerPane.add(spnMaxLev);
        graphLvlProbJFChartCtrlPanel.add(graphLvlProbSpinnerPane, BorderLayout.NORTH);
        
        GroupLayout grpLyoSubPrb = new GroupLayout(localBlockLvlProbGraph);
        localBlockLvlProbGraph.setLayout(grpLyoSubPrb);
        grpLyoSubPrb.setAutoCreateGaps(true);
        grpLyoSubPrb.setAutoCreateContainerGaps(true);
        grpLyoSubPrb.setHorizontalGroup(grpLyoSubPrb.createSequentialGroup()
            .addComponent(graphLvlProbJFChartChartPanel)
            .addComponent(graphLvlProbJFChartCtrlPanel));
        grpLyoSubPrb.setVerticalGroup(grpLyoSubPrb.createParallelGroup(
                GroupLayout.Alignment.CENTER)
            .addComponent(graphLvlProbJFChartChartPanel)
            .addComponent(graphLvlProbJFChartCtrlPanel));
        
        // NB: The listeners must be defined here because we first have to 
        //     built all the pieces (plot + parameters) and then define how
        //     things change upon change of the parameters/controllers.
 
        spnPar12.addChangeListener(new ChangeListener()
        {
            public void stateChanged(ChangeEvent event)
            {
                updateSubsProbDataset();
            }
        });
        spnPar13.addChangeListener(new ChangeListener()
        {
            public void stateChanged(ChangeEvent event)
            {
                updateSubsProbDataset();
            }
        });
        spnPar14.addChangeListener(new ChangeListener()
        {
            public void stateChanged(ChangeEvent event)
            {
                updateSubsProbDataset();
            }
        });
        
        cmbPar11.addActionListener(new ActionListener(){
            public void actionPerformed(ActionEvent e){
                switch (ProbabilityFuncitonShape.valueOf(
                        cmbPar11.getSelectedItem().toString()))
                {
                    case EXP_DIFF:
                        updateSubsProbDataset();
                        localBlockLvlProb3.setVisible(true);
                        localBlockLvlProb4.setVisible(false);
                        localBlockLvlProbGraph.setVisible(true);
                        break;
                        
                    case TANH:
                        updateSubsProbDataset();
                        localBlockLvlProb3.setVisible(true);
                        localBlockLvlProb4.setVisible(false);  
                        localBlockLvlProbGraph.setVisible(true);
                        break;
                        
                    case SIGMA:
                        updateSubsProbDataset();
                        localBlockLvlProb3.setVisible(false);
                        localBlockLvlProb4.setVisible(true);
                        localBlockLvlProbGraph.setVisible(true);
                        break;
                        
                    default:
                        localBlockLvlProb3.setVisible(false);
                        localBlockLvlProb4.setVisible(false); 
                        localBlockLvlProbGraph.setVisible(false);
                        break;
                }
            }
        });
        linePar11.add(lblPar11);
        linePar11.add(cmbPar11);
        localBlockLvlProbAll.add(linePar11);
        localBlockLvlProbAll.add(localBlockLvlProb3);
        localBlockLvlProbAll.add(localBlockLvlProb4);
        localBlockLvlProbAll.add(localBlockLvlProbGraph);
        localBlock2.add(localBlockLvlProbAll);
        
        String toolTipParMolSz2 = "<html>Specifies the value of the factor used in"
                + " molecular growth probability schemes <code>"
                + ProbabilityFuncitonShape.EXP_DIFF + "</code> and "
                + "<code>" 
                + ProbabilityFuncitonShape.TANH + "</code></html>";
        lineParMolSz2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblParMolSz2 = new JLabel("<html>Mol growth probability - parameter "
                + "<code>&lambda;</code><html>", SwingConstants.LEFT);
        lblParMolSz2.setPreferredSize(fileLabelSize);
        lblParMolSz2.setToolTipText(toolTipParMolSz2);
        spnParMolSz2 = new JSpinner(new SpinnerNumberModel(1.0, 0.0, null, 0.1));
        spnParMolSz2.setToolTipText(toolTipParMolSz2);
        spnParMolSz2.setPreferredSize(strFieldSize);
        mapKeyFieldToValueField.put(keyParMolSz2.toUpperCase(),spnParMolSz2);
        lineParMolSz2.add(lblParMolSz2);
        lineParMolSz2.add(spnParMolSz2);
        localBlockMolSz3.add(lineParMolSz2);
 
        String toolTipParMolSz3 = "<html>Specifies the value of parameter "
                + "&sigma;<sub>1</sub> used for molecular growth probability "
                + "scheme"
                + " <code>"
                + ProbabilityFuncitonShape.SIGMA
                + "</code>.<br>It corresponds to the steepness of"
                + " the function where <i>P(level) = 50%</i></html>";
        lineParMolSz3 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblParMolSz3 = new JLabel("<html>Mol growth probability - parameter "
                + "<code>&sigma;</code><sub>1</sub>:</html>", SwingConstants.LEFT);
        lblParMolSz3.setPreferredSize(fileLabelSize);
        lblParMolSz3.setToolTipText(toolTipParMolSz3);
        spnParMolSz3 = new JSpinner(new SpinnerNumberModel(0.2, null, null, 0.1));
        spnParMolSz3.setToolTipText(toolTipParMolSz3);
        spnParMolSz3.setPreferredSize(strFieldSize);
        mapKeyFieldToValueField.put(keyParMolSz3.toUpperCase(),spnParMolSz3);
        lineParMolSz3.add(lblParMolSz3);
        lineParMolSz3.add(spnParMolSz3);
        localBlockMolSz4.add(lineParMolSz3);
 
        String toolTipParMolSz4 = "<html>Specifies the value of parameter "
                + "&sigma;<sub>2</sub> used in molecular growth probability "
                + "scheme "
                + "<code>"
                + ProbabilityFuncitonShape.SIGMA 
                + "</code>.<br>It corresponds to the level "
                + "where <i>P(level) = 50%</i></html>";
        lineParMolSz4 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblParMolSz4 = new JLabel("<html>Mol growth probability - parameter "
                + "<code>&sigma;</code><sub>2</sub>:<html>", SwingConstants.LEFT);
        lblParMolSz4.setPreferredSize(fileLabelSize);
        lblParMolSz4.setToolTipText(toolTipParMolSz4);
        spnParMolSz4 = new JSpinner(new SpinnerNumberModel(25.0, null, null, 1.0));
        spnParMolSz4.setToolTipText(toolTipParMolSz4);
        spnParMolSz4.setPreferredSize(strFieldSize);
        mapKeyFieldToValueField.put(keyParMolSz4.toUpperCase(),spnParMolSz4);
        lineParMolSz4.add(lblParMolSz4);
        lineParMolSz4.add(spnParMolSz4);
        localBlockMolSz4.add(lineParMolSz4);
 
        String toolTipParMolSz1 = "Specifies the molecular growth probability scheme";
        lineParMolSz1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblParMolSz1 = new JLabel("Mol growth probability function:",
                SwingConstants.LEFT);
        lblParMolSz1.setPreferredSize(fileLabelSize);
        lblParMolSz1.setToolTipText(toolTipParMolSz1);
        cmbParMolSz1 = new JComboBox<ProbabilityFuncitonShape>(
                ProbabilityFuncitonShape.values());
        cmbParMolSz1.setSelectedItem(ProbabilityFuncitonShape.SIGMA);
        cmbParMolSz1.setToolTipText(toolTipParMolSz1);
        cmbParMolSz1.addActionListener(cmbFieldChange);
        mapKeyFieldToValueField.put(keyParMolSz1.toUpperCase(),cmbParMolSz1);
 
        // NB: we need to create the graph before setting the action listeners
        //     that will eventually edit the data plotted.
        createMolSzProbGraph();
 
        graphMolSzProbJFChartCtrlPanel = new JPanel(new BorderLayout());
        graphMolSzProbJFChartCtrlPanel.setMaximumSize(new Dimension(100,100));
        graphMolSzProbSpinnerPane = new JPanel(new GridLayout(0,2));
        final JSpinner spnMaxLevMolSz = new JSpinner(new SpinnerNumberModel(
                maxMolSizeProbPlot.intValue(), 1, null, 1));
        spnMaxLevMolSz.addChangeListener(new ChangeListener()
        {
            @Override
            public void stateChanged(ChangeEvent event)
            {
                int maxLev = ((Integer) spnMaxLevMolSz.getValue()).intValue();
                ((XYPlot) graphMolSzProbJFChart.getPlot())
                    .getDomainAxis().setRange(minMolSizeProbPlot, maxLev);
            }
        });
        graphMolSzProbSpinnerPane.add(new JLabel("X-axis max: "));
        graphMolSzProbSpinnerPane.add(spnMaxLevMolSz);
        graphMolSzProbJFChartCtrlPanel.add(graphMolSzProbSpinnerPane, BorderLayout.NORTH);
 
        GroupLayout grpLyoMolSzProb = new GroupLayout(localBlockMolSzGraph);
        localBlockMolSzGraph.setLayout(grpLyoMolSzProb);
        grpLyoMolSzProb.setAutoCreateGaps(true);
        grpLyoMolSzProb.setAutoCreateContainerGaps(true);
        grpLyoMolSzProb.setHorizontalGroup(grpLyoMolSzProb.createSequentialGroup()
            .addComponent(graphMolSzProbJFChartChartPanel)
            .addComponent(graphMolSzProbJFChartCtrlPanel));
        grpLyoMolSzProb.setVerticalGroup(grpLyoMolSzProb.createParallelGroup(
                GroupLayout.Alignment.CENTER)
            .addComponent(graphMolSzProbJFChartChartPanel)
            .addComponent(graphMolSzProbJFChartCtrlPanel));
 
        // NB: The listeners must be defined here because we first have to
        //     built all the pieces (plot + parameters) and then define how
        //     things change upon change of the parameters/controllers.
 
        spnParMolSz2.addChangeListener(new ChangeListener()
        {
            public void stateChanged(ChangeEvent event)
            {
                updatemolSizeProbDataset();
            }
        });
        spnParMolSz3.addChangeListener(new ChangeListener()
        {
            public void stateChanged(ChangeEvent event)
            {
                updatemolSizeProbDataset();
            }
        });
        spnParMolSz4.addChangeListener(new ChangeListener()
        {
            public void stateChanged(ChangeEvent event)
            {
                updatemolSizeProbDataset();
            }
        });
 
        cmbParMolSz1.addActionListener(new ActionListener(){
            public void actionPerformed(ActionEvent e){
                switch (ProbabilityFuncitonShape.valueOf(
                        cmbParMolSz1.getSelectedItem().toString()))
                {
                    case EXP_DIFF:
                        updatemolSizeProbDataset();
                        localBlockMolSz3.setVisible(true);
                        localBlockMolSz4.setVisible(false);
                        localBlockMolSzGraph.setVisible(true);
                        break;
 
                    case TANH:
                        updatemolSizeProbDataset();
                        localBlockMolSz3.setVisible(true);
                        localBlockMolSz4.setVisible(false);
                        localBlockMolSzGraph.setVisible(true);
                        break;
 
                    case SIGMA:
                        updatemolSizeProbDataset();
                        localBlockMolSz3.setVisible(false);
                        localBlockMolSz4.setVisible(true);
                        localBlockMolSzGraph.setVisible(true);
                        break;
 
                    case UNRESTRICTED:
                        updatemolSizeProbDataset();
                        localBlockMolSz3.setVisible(false);
                        localBlockMolSz4.setVisible(false);
                        localBlockMolSzGraph.setVisible(true);
                        break;
 
                    default:
                        localBlockMolSz3.setVisible(false);
                        localBlockMolSz4.setVisible(false);
                        localBlockMolSzGraph.setVisible(false);
                        break;
                }
            }
        });
        lineParMolSz1.add(lblParMolSz1);
        lineParMolSz1.add(cmbParMolSz1);
        localBlockMolSzAll.add(lineParMolSz1);
        localBlockMolSzAll.add(localBlockMolSz3);
        localBlockMolSzAll.add(localBlockMolSz4);
        localBlockMolSzAll.add(localBlockMolSzGraph);
        
        localBlock2.add(localBlockMolSzAll);
 
        localBlock2.add(new JSeparator());
        
        String toolTipParCrowd2 = "<html>Specifies the value of the factor used in"
                + " crowding probability schemes <code>"
                + ProbabilityFuncitonShape.EXP_DIFF
                + "</code> and "
                + "<code>"
                + ProbabilityFuncitonShape.TANH
                + "</code></html>";
        lineParCrowd2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblParCrowd2 = new JLabel("<html>Crowding probability - parameter "
                + "<code>&lambda;</code><html>", SwingConstants.LEFT);
        lblParCrowd2.setPreferredSize(fileLabelSize);
        lblParCrowd2.setToolTipText(toolTipParCrowd2);
        spnParCrowd2 = new JSpinner(new SpinnerNumberModel(1.0, 0.0, null, 0.1));
        spnParCrowd2.setToolTipText(toolTipParCrowd2);
        spnParCrowd2.setPreferredSize(strFieldSize);
        mapKeyFieldToValueField.put(keyParCrowd2.toUpperCase(),spnParCrowd2);
        lineParCrowd2.add(lblParCrowd2);
        lineParCrowd2.add(spnParCrowd2);
        localBlockCrowd3.add(lineParCrowd2);
        
        String toolTipParCrowd3 = "<html>Specifies the value of parameter "
                + "&sigma;<sub>1</sub> used for crowding probability scheme"
                + " <code>"
                + ProbabilityFuncitonShape.SIGMA
                + "</code>.<br>It corresponds to the steepness of"
                + " the function where <i>P(level) = 50%</i></html>";
        lineParCrowd3 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblParCrowd3 = new JLabel("<html>Crowding probability - parameter "
                + "<code>&sigma;</code><sub>1</sub>:</html>", SwingConstants.LEFT);
        lblParCrowd3.setPreferredSize(fileLabelSize);
        lblParCrowd3.setToolTipText(toolTipParCrowd3);
        spnParCrowd3 = new JSpinner(new SpinnerNumberModel(1.0, null, null, 0.1));
        spnParCrowd3.setToolTipText(toolTipParCrowd3);
        spnParCrowd3.setPreferredSize(strFieldSize);
        mapKeyFieldToValueField.put(keyParCrowd3.toUpperCase(),spnParCrowd3);
        lineParCrowd3.add(lblParCrowd3);
        lineParCrowd3.add(spnParCrowd3);
        localBlockCrowd4.add(lineParCrowd3);
        
        String toolTipParCrowd4 = "<html>Specifies the value of parameter "
                + "&sigma;<sub>2</sub> used in crowding probability scheme "
                + "<code>"
                + ProbabilityFuncitonShape.SIGMA
                + "</code>.<br>It corresponds to the level "
                + "where <i>P(level) = 50%</i></html>";
        lineParCrowd4 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblParCrowd4 = new JLabel("<html>Crowding probability - parameter "
                + "<code>&sigma;</code><sub>2</sub>:<html>", SwingConstants.LEFT);
        lblParCrowd4.setPreferredSize(fileLabelSize);
        lblParCrowd4.setToolTipText(toolTipParCrowd4);
        spnParCrowd4 = new JSpinner(new SpinnerNumberModel(3.5, null, null, 0.1));
        spnParCrowd4.setToolTipText(toolTipParCrowd4);
        spnParCrowd4.setPreferredSize(strFieldSize);
        mapKeyFieldToValueField.put(keyParCrowd4.toUpperCase(),spnParCrowd4);
        lineParCrowd4.add(lblParCrowd4);
        lineParCrowd4.add(spnParCrowd4);
        localBlockCrowd4.add(lineParCrowd4);
        
        String toolTipParCrowd1 = "Specifies the crowding probability scheme";
        lineParCrowd1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblParCrowd1 = new JLabel("Crowding probability function:", 
                SwingConstants.LEFT);
        lblParCrowd1.setPreferredSize(fileLabelSize);
        lblParCrowd1.setToolTipText(toolTipParCrowd1);
        cmbParCrowd1 = new JComboBox<ProbabilityFuncitonShape>(
                ProbabilityFuncitonShape.values());
        cmbParCrowd1.setSelectedItem(ProbabilityFuncitonShape.UNRESTRICTED);
        cmbParCrowd1.setToolTipText(toolTipParCrowd1);
        cmbParCrowd1.addActionListener(cmbFieldChange);
        mapKeyFieldToValueField.put(keyParCrowd1.toUpperCase(),cmbParCrowd1);
        
        // NB: we need to create the graph before setting the action listeners
        //     that will eventually edit the data plotted.
        createCrowdProbGraph();
        
        graphCrowdProbJFChartCtrlPanel = new JPanel(new BorderLayout());
        graphCrowdProbJFChartCtrlPanel.setMaximumSize(new Dimension(100,100));
        graphCrowdProbSpinnerPane = new JPanel(new GridLayout(0,2));
        final JSpinner spnMaxLevCrowd = new JSpinner(new SpinnerNumberModel(
                maxLevelCrowdProbPlot.intValue(), 1, null, 1));
        spnMaxLevCrowd.addChangeListener(new ChangeListener()
        {
            @Override
            public void stateChanged(ChangeEvent event)
            {
                int maxLev = ((Integer) spnMaxLevCrowd.getValue()).intValue();                
                ((XYPlot) graphCrowdProbJFChart.getPlot())
                    .getDomainAxis().setRange(minLevelCrowdProbPlot, maxLev);
            }
        }); 
        graphCrowdProbSpinnerPane.add(new JLabel("X-axis max: "));
        graphCrowdProbSpinnerPane.add(spnMaxLevCrowd);
        graphCrowdProbJFChartCtrlPanel.add(graphCrowdProbSpinnerPane, BorderLayout.NORTH);
        
        GroupLayout grpLyoCrowdProb = new GroupLayout(localBlockCrowdGraph);
        localBlockCrowdGraph.setLayout(grpLyoCrowdProb);
        grpLyoCrowdProb.setAutoCreateGaps(true);
        grpLyoCrowdProb.setAutoCreateContainerGaps(true);
        grpLyoCrowdProb.setHorizontalGroup(grpLyoCrowdProb.createSequentialGroup()
            .addComponent(graphCrowdProbJFChartChartPanel)
            .addComponent(graphCrowdProbJFChartCtrlPanel));
        grpLyoCrowdProb.setVerticalGroup(grpLyoCrowdProb.createParallelGroup(
                GroupLayout.Alignment.CENTER)
            .addComponent(graphCrowdProbJFChartChartPanel)
            .addComponent(graphCrowdProbJFChartCtrlPanel));
        
        // NB: The listeners must be defined here because we first have to 
        //     built all the pieces (plot + parameters) and then define how
        //     things change upon change of the parameters/controllers.
 
        spnParCrowd2.addChangeListener(new ChangeListener()
        {
            public void stateChanged(ChangeEvent event)
            {
                updateCrowdProbDataset();
            }
        });
        spnParCrowd3.addChangeListener(new ChangeListener()
        {
            public void stateChanged(ChangeEvent event)
            {
                updateCrowdProbDataset();
            }
        });
        spnParCrowd4.addChangeListener(new ChangeListener()
        {
            public void stateChanged(ChangeEvent event)
            {
                updateCrowdProbDataset();
            }
        });
        
        cmbParCrowd1.addActionListener(new ActionListener(){
            public void actionPerformed(ActionEvent e){
                String scheme = cmbParCrowd1.getSelectedItem().toString();
                switch (ProbabilityFuncitonShape.valueOf(scheme))
                {
                    case EXP_DIFF:
                        updateCrowdProbDataset();
                        localBlockCrowd3.setVisible(true);
                        localBlockCrowd4.setVisible(false);
                        localBlockCrowdGraph.setVisible(true);
                        break;
                        
                    case TANH:
                        updateCrowdProbDataset();
                        localBlockCrowd3.setVisible(true);
                        localBlockCrowd4.setVisible(false);  
                        localBlockCrowdGraph.setVisible(true);
                        break;
                        
                    case SIGMA:
                        updateCrowdProbDataset();
                        localBlockCrowd3.setVisible(false);
                        localBlockCrowd4.setVisible(true);
                        localBlockCrowdGraph.setVisible(true);
                        break;
                        
                    case UNRESTRICTED:
                        updateCrowdProbDataset();
                        localBlockCrowd3.setVisible(false);
                        localBlockCrowd4.setVisible(false);
                        localBlockCrowdGraph.setVisible(true);
                        break;
                        
                    default:
                        localBlockCrowd3.setVisible(false);
                        localBlockCrowd4.setVisible(false); 
                        localBlockCrowdGraph.setVisible(false);
                        break;
                }
            }
        });
        lineParCrowd1.add(lblParCrowd1);
        lineParCrowd1.add(cmbParCrowd1);
        localBlock2.add(lineParCrowd1);
        localBlock2.add(localBlockCrowd3);
        localBlock2.add(localBlockCrowd4);
        localBlock2.add(localBlockCrowdGraph);
        
        localBlock2.add(new JSeparator());
 
        String toolTipPar15 = "<html>Specifies the strategy for selecting crossover partners.<ul>" 
                + "<li><code>RANDOM</code>: unbiased selection.</li>" 
                + "<li><code>TS</code>: Tournament.</li>" 
                + "<li><code>RW</code>: Roulette Wheel.</li>" 
                + "<li><code>SUS</code>: Stochastic Universal Sampling.</li>"
                + "</ul></html>";
        linePar15 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar15 = new JLabel("Parent selection algorithm:", SwingConstants.LEFT);
        lblPar15.setPreferredSize(fileLabelSize);
        lblPar15.setToolTipText(toolTipPar15);
        cmbPar15 = new JComboBox<String>(new String[] {"RANDOM", "TS", "RW", "SUS"});
        cmbPar15.setToolTipText(toolTipPar15);
        cmbPar15.addActionListener(cmbFieldChange);
        mapKeyFieldToValueField.put(keyPar15.toUpperCase(),cmbPar15);
        linePar15.add(lblPar15);
        linePar15.add(cmbPar15);
        localBlock2.add(linePar15);
 
        String toolTipPar16 = "<html>Specifies the relative weight of "
                + "crossover operations.</html>";
        linePar16 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar16 = new JLabel("Crossover weight:", SwingConstants.LEFT);
        lblPar16.setPreferredSize(fileLabelSize);
        lblPar16.setToolTipText(toolTipPar16);
        txtPar16 = new JTextField();
        txtPar16.setToolTipText(toolTipPar16);
        txtPar16.setPreferredSize(strFieldSize);
        txtPar16.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar16.toUpperCase(),txtPar16);
        linePar16.add(lblPar16);
        linePar16.add(txtPar16);
        localBlock2.add(linePar16);
 
        String toolTipPar17 = "<html>Specifies the relative weight of "
                + "mutation operations.</html>";
        linePar17 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar17 = new JLabel("Mutation weight:", SwingConstants.LEFT);
        lblPar17.setPreferredSize(fileLabelSize);
        lblPar17.setToolTipText(toolTipPar17);
        txtPar17 = new JTextField();
        txtPar17.setToolTipText(toolTipPar17);
        txtPar17.setPreferredSize(strFieldSize);
        txtPar17.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar17.toUpperCase(),txtPar17);
        linePar17.add(lblPar17);
        linePar17.add(txtPar17);
        localBlock2.add(linePar17);
        
        String toolTipParWC = "<html>Specifies the relative weight of "
                + "construction from scratch.</html>";
        lineParWC = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblParWC = new JLabel("Construction weight:", SwingConstants.LEFT);
        lblParWC.setPreferredSize(fileLabelSize);
        lblParWC.setToolTipText(toolTipParWC);
        txtParWC = new JTextField();
        txtParWC.setToolTipText(toolTipParWC);
        txtParWC.setPreferredSize(strFieldSize);
        txtParWC.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyParWC.toUpperCase(),txtParWC);
        lineParWC.add(lblParWC);
        lineParWC.add(txtParWC);
        localBlock2.add(lineParWC);
 
        String toolTipPar18 = "Specifies the probability (0.0-1.0) of symmetric operations.";
        linePar18 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar18 = new JLabel("Symmetric operation probability:", SwingConstants.LEFT);
        lblPar18.setPreferredSize(fileLabelSize);
        lblPar18.setToolTipText(toolTipPar18);
        txtPar18 = new JTextField();
        txtPar18.setToolTipText(toolTipPar18);
        txtPar18.setPreferredSize(strFieldSize);
        txtPar18.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar18.toUpperCase(),txtPar18);
        linePar18.add(lblPar18);
        linePar18.add(txtPar18);
        localBlock2.add(linePar18);
 
        String toolTipPar19 = "Specifies the population members replacement strategy.";
        linePar19 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar19 = new JLabel("Population update mode:", SwingConstants.LEFT);
        lblPar19.setPreferredSize(fileLabelSize);
        lblPar19.setToolTipText(toolTipPar19);
        cmbPar19 = new JComboBox<String>(new String[] {"ELITIST", "NONE"});
        cmbPar19.setToolTipText(toolTipPar19);
        cmbPar19.addActionListener(cmbFieldChange);
        mapKeyFieldToValueField.put(keyPar19.toUpperCase(),cmbPar19);
        linePar19.add(lblPar19);
        linePar19.add(cmbPar19);
        localBlock2.add(linePar19);
 
        String toolTipPar24 = "Specifies the maximum number of parallel candidate evaluation tasks.";
        linePar24 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar24 = new JLabel("Number of parallel evaluation tasks:", SwingConstants.LEFT);
        lblPar24.setPreferredSize(fileLabelSize);
        lblPar24.setToolTipText(toolTipPar24);
        txtPar24 = new JTextField();
        txtPar24.setToolTipText(toolTipPar24);
        txtPar24.setPreferredSize(strFieldSize);
        txtPar24.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar24.toUpperCase(),txtPar24);
        linePar24.add(lblPar24);
        linePar24.add(txtPar24);
        localBlock2.add(linePar24);
 
        String toolTipPar25 = "<html>Specifies the parallelization scheme:<br><ul><li><code>synchronous</code>, i.e., parallel tasks are submitted in batches, thus no new task is submitted until the last of the previous tasks is completed.</li><li><code>asynchronous</code>, i.e., a new parallel tasks is submitted as soon as any of the previous task is completed.</li></ul></html>";
        linePar25 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar25 = new JLabel("Task parallelization scheme:", SwingConstants.LEFT);
        lblPar25.setPreferredSize(fileLabelSize);
        lblPar25.setToolTipText(toolTipPar25);
        cmbPar25 = new JComboBox<String>(new String[] {"Synchronous", "Asynchronous"});
        cmbPar25.setToolTipText(toolTipPar25);
        cmbPar25.addActionListener(cmbFieldChange);
        mapKeyFieldToValueField.put(keyPar25.toUpperCase(),cmbPar25);
        linePar25.add(lblPar25);
        linePar25.add(cmbPar25);
        localBlock2.add(linePar25);
 
        // From here it's all about advanced options
        
        String toolTipParMSM = "<html>Specifies the relative weight of "
                + "multi-site mutation operations "
                + "(comma- or space-separated list).</html>";
        lineParMSM = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblParMSM = new JLabel("Multi-site mutation weight:", SwingConstants.LEFT);
        lblParMSM.setPreferredSize(fileLabelSize);
        lblParMSM.setToolTipText(toolTipParMSM);
        txtParMSM = new JTextField();
        txtParMSM.setToolTipText(toolTipParMSM);
        txtParMSM.setPreferredSize(strFieldSize);
        txtParMSM.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyParMSM.toUpperCase(),txtParMSM);
        lineParMSM.add(lblParMSM);
        lineParMSM.add(txtParMSM);
        advOptsBlock.add(lineParMSM);
 
        String toolTipPar3 = "Specifies the seed number used by the random number generator";
        linePar3 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar3 = new JLabel("Random Seed:", SwingConstants.LEFT);
        lblPar3.setPreferredSize(fileLabelSize);
        lblPar3.setToolTipText(toolTipPar3);
        txtPar3 = new JTextField();
        txtPar3.setToolTipText(toolTipPar3);
        txtPar3.setPreferredSize(new Dimension(150,preferredHeight));
        txtPar3.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar3.toUpperCase(),txtPar3);
        linePar3.add(lblPar3);
        linePar3.add(txtPar3);
        advOptsBlock.add(linePar3);
 
        String toolTipPar1 = "Specifies the number of figures used to report the fitness";
        linePar1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar1 = new JLabel("Precision of fitness value:", SwingConstants.LEFT);
        lblPar1.setPreferredSize(fileLabelSize);
        lblPar1.setToolTipText(toolTipPar1);
        txtPar1 = new JTextField();
        txtPar1.setToolTipText(toolTipPar1);
        txtPar1.setPreferredSize(strFieldSize);
        txtPar1.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar1.toUpperCase(),txtPar1);
        linePar1.add(lblPar1);
        linePar1.add(txtPar1);
        advOptsBlock.add(linePar1);
 
        String toolTipPar2 = "Specifies the amount of log produced.";
        linePar2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar2 = new JLabel("Verbosity of GA modules:", SwingConstants.LEFT);
        lblPar2.setPreferredSize(fileLabelSize);
        lblPar2.setToolTipText(toolTipPar2);
        cmbPar2 = new JComboBox<String>(new String[] {"-3", "-2", "-1", "0", "1", "2", "3"});
        cmbPar2.setToolTipText(toolTipPar2);
        cmbPar2.setSelectedItem("0");
        cmbPar2.addActionListener(cmbFieldChange);
        mapKeyFieldToValueField.put(keyPar2.toUpperCase(),cmbPar2);
        linePar2.add(lblPar2);
        linePar2.add(cmbPar2);
        advOptsBlock.add(linePar2);
 
        String toolTipPar5 = "Specifies whether the candidates should be reported in descending or ascending order of fitness.";
        linePar5 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        rdbPar5 = new JRadioButton("Sort by descending fitness");
        rdbPar5.setToolTipText(toolTipPar5);
        rdbPar5.addChangeListener(rdbFieldChange);
        mapKeyFieldToValueField.put(keyPar5.toUpperCase(),rdbPar5);
        linePar5.add(rdbPar5);
        advOptsBlock.add(linePar5);
 
        String toolTipPar5a = "Specifies whether a NaN fitness value should stop the design experiment.";
        linePar5a = new JPanel(new FlowLayout(FlowLayout.LEFT));
        rdbPar5a = new JRadioButton("Kill experiment on NaN fitness");
        rdbPar5a.setToolTipText(toolTipPar5a);
        rdbPar5a.addChangeListener(rdbFieldChange);
        mapKeyFieldToValueField.put(keyPar5a.toUpperCase(),rdbPar5a);
        linePar5a.add(rdbPar5a);
        advOptsBlock.add(linePar5a);
 
        String toolTipPar10 = "<html>Controls the maximum number of attempts to build a new graph.<br> The maximum number of attempts to build a new graph is given by the size of the population, times this factor.</html>";
        linePar10 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar10 = new JLabel("Max tries to get new graph:", SwingConstants.LEFT);
        lblPar10.setPreferredSize(fileLabelSize);
        lblPar10.setToolTipText(toolTipPar10);
        txtPar10 = new JTextField();
        txtPar10.setToolTipText(toolTipPar10);
        txtPar10.setPreferredSize(strFieldSize);
        txtPar10.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar10.toUpperCase(),txtPar10);
        linePar10.add(lblPar10);
        linePar10.add(txtPar10);
        advOptsBlock.add(linePar10);
        
 
        advOptsBlock.add(new JSeparator());
        
        
        String toolMolToGraph = "<html>Specifies the pathname of a file containing molecules that should be screened to generate the initial population.<br> The file can be an SDF file or a text file where each line contains a SMILES.</html>";
        lineMolToGraph = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblMolToGraph = new JLabel("Initial population from screening:", SwingConstants.LEFT);
        lblMolToGraph.setPreferredSize(fileLabelSize);
        lblMolToGraph.setToolTipText(toolMolToGraph);
        txtMolToGraph = new JTextField();
        txtMolToGraph.setToolTipText(toolMolToGraph);
        txtMolToGraph.setPreferredSize(fileFieldSize);
        txtMolToGraph.getDocument().addDocumentListener(fieldListener);
        txtMolToGraph.getDocument().addDocumentListener(new DocumentListener() {
            public void changedUpdate(DocumentEvent e) {
                if (txtMolToGraph.getText().isBlank())
                {
                    txtFrgMols.setEnabled(false);
                    btnFrgMols.setEnabled(false);
                    rdbAddH.setEnabled(false);
                } else {
                    txtFrgMols.setEnabled(true);
                    btnFrgMols.setEnabled(true);
                    rdbAddH.setEnabled(true);
                }
            }
            public void removeUpdate(DocumentEvent e) {
                if (txtMolToGraph.getText().isBlank())
                {
                    txtFrgMols.setEnabled(false);
                    btnFrgMols.setEnabled(false);
                    rdbAddH.setEnabled(false);
                } else {
                    txtFrgMols.setEnabled(true);
                    btnFrgMols.setEnabled(true);
                    rdbAddH.setEnabled(true);
                }
            }
            public void insertUpdate(DocumentEvent e) {
                if (txtMolToGraph.getText().isBlank())
                {
                    txtFrgMols.setEnabled(false);
                    btnFrgMols.setEnabled(false);
                    rdbAddH.setEnabled(false);
                } else {
                    txtFrgMols.setEnabled(true);
                    btnFrgMols.setEnabled(true);
                    rdbAddH.setEnabled(true);
                }
            }
        });
        mapKeyFieldToValueField.put(keyMolToGraph.toUpperCase(), txtMolToGraph);
        btnMolToGraph = new JButton("Browse");
        btnMolToGraph.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
                GUIFileOpener.pickFileForTxtField(txtMolToGraph,btnMolToGraph);
           }
        });
        lineMolToGraph.add(lblMolToGraph);
        lineMolToGraph.add(txtMolToGraph);
        lineMolToGraph.add(btnMolToGraph);
        advOptsBlock.add(lineMolToGraph);
        
        String toolFrgMols = "<html>Specifies the pathname of a file containing the cutting rules to apply when converting molecules into graphs</html>";
        lineFrgMols = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblFrgMols = new JLabel("Mol-to-graph bond-cutting rules:", SwingConstants.LEFT);
        lblFrgMols.setPreferredSize(fileLabelSize);
        lblFrgMols.setToolTipText(toolFrgMols);
        txtFrgMols = new JTextField();
        txtFrgMols.setToolTipText(toolFrgMols);
        txtFrgMols.setPreferredSize(fileFieldSize);
        txtFrgMols.getDocument().addDocumentListener(fieldListener);
        txtFrgMols.setEnabled(false);
        mapKeyFieldToValueField.put(keyFrgMols.toUpperCase(), txtFrgMols);
        btnFrgMols = new JButton("Browse");
        btnFrgMols.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
                GUIFileOpener.pickFileForTxtField(txtFrgMols, btnFrgMols);
           }
        });
        btnFrgMols.setEnabled(false);
        lineFrgMols.add(lblFrgMols);
        lineFrgMols.add(txtFrgMols);
        lineFrgMols.add(btnFrgMols);
        advOptsBlock.add(lineFrgMols);
        
        String toolAddH = "Specifies whether the to add explicit H atoms upon importing molecules to be fragmented.";
        lineAddH = new JPanel(new FlowLayout(FlowLayout.LEFT));
        rdbAddH = new JRadioButton("Add explicit H atoms");
        rdbAddH.setToolTipText(toolAddH);
        rdbAddH.addChangeListener(rdbFieldChange);
        rdbAddH.setEnabled(false);
        mapKeyFieldToValueField.put(keyAddH.toUpperCase(),rdbAddH);
        lineAddH.add(rdbAddH);
        advOptsBlock.add(lineAddH);
 
        
        advOptsBlock.add(new JSeparator());
 
        
        String toolTipPar20 = "<html>Specifies the pathname of a file containing previously evaluated individuals to be added to the initial population.<br> The file can be an SDF file or a text file where each line containing the pathname to a single-molecule SDF file.</html>";
        linePar20 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar20 = new JLabel("Initial population file (SDF):", SwingConstants.LEFT);
        lblPar20.setPreferredSize(fileLabelSize);
        lblPar20.setToolTipText(toolTipPar20);
        txtPar20 = new JTextField();
        txtPar20.setToolTipText(toolTipPar20);
        txtPar20.setPreferredSize(fileFieldSize);
        txtPar20.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar20.toUpperCase(),txtPar20);
        btnPar20 = new JButton("Browse");
        btnPar20.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
                GUIFileOpener.pickFileForTxtField(txtPar20,btnPar20);
           }
        });
        linePar20.add(lblPar20);
        linePar20.add(txtPar20);
        linePar20.add(btnPar20);
        advOptsBlock.add(linePar20);
 
        String toolTipPar21 = "<html>Specifies the pathname of a text file collecting unique individual identification (UID) of previously known individuals.<br>The file must have one UID per line.</html>";
        linePar21 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar21 = new JLabel("File with known UIDs:", SwingConstants.LEFT);
        lblPar21.setPreferredSize(fileLabelSize);
        lblPar21.setToolTipText(toolTipPar21);
        txtPar21 = new JTextField();
        txtPar21.setToolTipText(toolTipPar21);
        txtPar21.setPreferredSize(fileFieldSize);
        txtPar21.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar21.toUpperCase(),txtPar21);
        btnPar21 = new JButton("Browse");
        btnPar21.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
                GUIFileOpener.pickFileForTxtField(txtPar21,btnPar21);
           }
        });
        linePar21.add(lblPar21);
        linePar21.add(txtPar21);
        linePar21.add(btnPar21);
        advOptsBlock.add(linePar21);
 
        String toolTipPar22 = "Specifies the pathname of the file that will collect unique individual identification (UID) strings encountered during an evolutionary experiment.";
        linePar22 = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblPar22 = new JLabel("File for new UIDs:", SwingConstants.LEFT);
        lblPar22.setPreferredSize(fileLabelSize);
        lblPar22.setToolTipText(toolTipPar22);
        txtPar22 = new JTextField();
        txtPar22.setToolTipText(toolTipPar22);
        txtPar22.setPreferredSize(fileFieldSize);
        txtPar22.getDocument().addDocumentListener(fieldListener);
        mapKeyFieldToValueField.put(keyPar22.toUpperCase(),txtPar22);
        btnPar22 = new JButton("Browse");
        btnPar22.addActionListener(new ActionListener() {
        public void actionPerformed(ActionEvent e) {
                GUIFileOpener.pickFileForTxtField(txtPar22,btnPar22);
           }
        });
        linePar22.add(lblPar22);
        linePar22.add(txtPar22);
        linePar22.add(btnPar22);
        advOptsBlock.add(linePar22);
        
        advOptsBlock.add(new JSeparator());
        
        String toolTipRingTmplsFrags = "<html>Specifies whether ring systems "
                + "should be extracted <br>"
                + "from generated graphs and stored as new general-"
                + "purpose building blocks."
                + "</html>";
        lineRingTmplsFrags = new JPanel(new FlowLayout(FlowLayout.LEFT));
        rdbRingTmplsFrags = new JRadioButton("Add new ring systems to building "
                + "block library.");
        rdbRingTmplsFrags.setToolTipText(toolTipRingTmplsFrags);
        rdbRingTmplsFrags.addChangeListener(rdbFieldChange);
        mapKeyFieldToValueField.put(keyRingTmplsFrags.toUpperCase(),
                rdbRingTmplsFrags);
        lineRingTmplsFrags.add(rdbRingTmplsFrags);
        advOptsBlock.add(lineRingTmplsFrags);
        
        String toolTipRingTmplsScaff = "<html>Specifies whether ring systems "
                + "should be extracted <br>"
                + "from generated graphs and stored as new "
                + "scaffold building blocks."
                + "</html>";
        lineRingTmplsScaff = new JPanel(new FlowLayout(FlowLayout.LEFT));
        rdbRingTmplsScaff = new JRadioButton("Add new ring systems to library "
                + "of scaffold building blocks.");
        rdbRingTmplsScaff.setToolTipText(toolTipRingTmplsScaff);
        rdbRingTmplsScaff.addChangeListener(rdbFieldChange);
        mapKeyFieldToValueField.put(keyRingTmplsScaff.toUpperCase(),
                rdbRingTmplsScaff);
        lineRingTmplsScaff.add(rdbRingTmplsScaff);
        advOptsBlock.add(lineRingTmplsScaff);
        
        String toolTipRingSysTmpl = "<html>A %/100 defining how good "
                + "(high fitness w.r.t. population range)<br> "
                + "candidates need to be for generating "
                + "new ring system templates.<br>"
                + "For example, 0.10 "
                + "allows only the best 10% of the candidates <br>to generate "
                + "a new building block from theyr graph.</html>";
        lineRingSysTmpl = new JPanel(new FlowLayout(FlowLayout.LEFT));
        lblRingSysTmpl = new JLabel("Threshold for saving ring systems:", 
                SwingConstants.LEFT);
        lblRingSysTmpl.setPreferredSize(fileLabelSize);
        lblRingSysTmpl.setToolTipText(toolTipRingSysTmpl);
        spnRingSysTmpl = new JSpinner(new SpinnerNumberModel(0.10,0.0,1.0,0.05));
        spnRingSysTmpl.setToolTipText(toolTipRingSysTmpl);
        spnRingSysTmpl.setPreferredSize(strFieldSize);
        mapKeyFieldToValueField.put(keyRingSysTmplTrhld.toUpperCase(),
                spnRingSysTmpl);
        lineRingSysTmpl.add(lblRingSysTmpl);
        lineRingSysTmpl.add(spnRingSysTmpl);
        advOptsBlock.add(rdbRingTmplsFrags);
        advOptsBlock.add(rdbRingTmplsScaff);
        advOptsBlock.add(lineRingSysTmpl);
        
        advOptsBlock.add(super.getPanelForUnformattedInput());
        
 
        //HEREGOESADVIMPLEMENTATION this is only to facilitate automated insertion of code       
        
        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.add(advOptShow);
        localBlock2.add(new JSeparator());
        localBlock2.add(advOptsController);
        localBlock2.add(advOptsBlock);      
        
        this.add(scrollablePane);
    }
    
//-----------------------------------------------------------------------------
 
    private void updateSubsProbDataset() 
    {
        createLvlProbDataset();
        ((XYPlot) graphLvlProbJFChart.getPlot()).setDataset(levelProbData); 
    }
        
//-----------------------------------------------------------------------------
 
    private void createLvlProbDataset() 
    {   
        levelProbData = new DefaultXYDataset();
        
        ArrayList<Double> y = new ArrayList<Double>();
        try
        {
            int scheme = GAParameters.convertProbabilityScheme(
                    cmbPar11.getSelectedItem().toString());
            double l = (Double) spnPar12.getValue();
            double s1 = (Double) spnPar13.getValue();
            double s2 = (Double) spnPar14.getValue();
            
            for (int level=0; level<100; level++)
            {
                double prob = EAUtils.getGrowthProbabilityAtLevel(
                        level, scheme, l, s1, s2);
                y.add(prob);
            }
        }
        catch (Exception e)
        {
            e.printStackTrace();
            JOptionPane.showMessageDialog(this,
                    "<html>Exception occurred while reading growth proability "
                    + "scheme.<br>"
                    + "Please, report this to the DENOPTIM team.</html>",
                    "Error",
                    JOptionPane.ERROR_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
        }
 
        double[][] data = new double[2][y.size()];
        for (int level=0; level<100; level++)
        {
            data[0][level] = level;
            data[1][level] = y.get(level);
        }
        
        levelProbData.addSeries("Growth Probability", data);
    }
    
//-----------------------------------------------------------------------------
 
    private void createLvlProbGraph() 
    {
        createLvlProbDataset();
        createLvlProbChart();
        graphLvlProbJFChartChartPanel = new ChartPanel(graphLvlProbJFChart);
        graphLvlProbJFChartChartPanel.setMaximumSize(new Dimension(400,200));
    }
    
//-----------------------------------------------------------------------------
    
    private void createLvlProbChart()
    {
        graphLvlProbJFChart = ChartFactory.createXYLineChart(
            null,                         // plot title
            "Level",                      // x axis label
            "Probability",                // y axis label
            levelProbData,                 // data
            PlotOrientation.VERTICAL,  
            false,                        // include legend
            false,                        // tooltips
            false                         // urls
        );
 
        XYPlot plot = (XYPlot) graphLvlProbJFChart.getPlot();
        
        // axis ranges
        plot.getDomainAxis().setRange(minLevelProbPlot, maxLevelProbPlot);
        plot.getRangeAxis().setRange(0.0, 1.0);
        
        // axis ticks interval 
        //NB: this if commented out because it blocks automated selection of tick units
        // and therefore it allows ticks overlap when range is large
        //((NumberAxis) plot.getDomainAxis()).setTickUnit(new NumberTickUnit(1.0));
 
        // series line thickness
        XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
        renderer.setSeriesPaint(0, Color.decode("#490092"));
        renderer.setSeriesStroke(0, new BasicStroke(2.0f));
        plot.setRenderer(renderer);
        
        // font of axis label
        Font font3 = new Font("Dialog", Font.PLAIN, 12); 
        plot.getDomainAxis().setLabelFont(font3);
        plot.getRangeAxis().setLabelFont(font3);
    }
    
  //-----------------------------------------------------------------------------
 
    private void updatemolSizeProbDataset()
    {
        createMolSizeProbDataset();
        ((XYPlot) graphMolSzProbJFChart.getPlot()).setDataset(molSizeProbData);
    }
 
//-----------------------------------------------------------------------------
 
    private void createMolSizeProbDataset()
    {
        molSizeProbData = new DefaultXYDataset();
 
        ArrayList<Double> y = new ArrayList<Double>();
        try
        {
          int scheme = GAParameters.convertProbabilityScheme(
                  cmbParMolSz1.getSelectedItem().toString());
          double l = (Double) spnParMolSz2.getValue();
          double s1 = (Double) spnParMolSz3.getValue();
          double s2 = (Double) spnParMolSz4.getValue();
 
          for (int numHeavyAtoms=0; numHeavyAtoms<100; numHeavyAtoms++)
          {
                double prob = EAUtils.getProbability(
                        numHeavyAtoms, scheme, l, s1, s2);
                y.add(prob);
          }
        }
        catch (Exception e)
        {
          e.printStackTrace();
          JOptionPane.showMessageDialog(this,
                  "<html>Exception occurred while reading croding proability "
                  + "scheme.<br>"
                  + "Please, report this to the DENOPTIM team.</html>",
                  "Error",
                  JOptionPane.ERROR_MESSAGE,
                  UIManager.getIcon("OptionPane.errorIcon"));
        }
 
        double[][] data = new double[2][y.size()];
        for (int numHeavyAtoms=0; numHeavyAtoms<100; numHeavyAtoms++)
        {
          data[0][numHeavyAtoms] = numHeavyAtoms;
          data[1][numHeavyAtoms] = y.get(numHeavyAtoms);
        }
 
        molSizeProbData.addSeries("Mol Growth Probability", data);
    }
 
//-----------------------------------------------------------------------------
 
    private void createMolSzProbGraph()
    {
        createMolSizeProbDataset();
        createMolSzProbChart();
        graphMolSzProbJFChartChartPanel = new ChartPanel(graphMolSzProbJFChart);
        graphMolSzProbJFChartChartPanel.setMaximumSize(new Dimension(400,200));
    }
 
//-----------------------------------------------------------------------------
 
    private void createMolSzProbChart()
    {
        graphMolSzProbJFChart = ChartFactory.createXYLineChart(
          null,                     // plot title
          "# Heavy Atoms",                // x axis label
          "Probability",                // y axis label
          molSizeProbData,                 // data
          PlotOrientation.VERTICAL,
          false,                    // include legend
          false,                    // tooltips
          false                     // urls
        );
 
        XYPlot plot = (XYPlot) graphMolSzProbJFChart.getPlot();
 
        // axis ranges
        plot.getDomainAxis().setRange(minMolSizeProbPlot, maxMolSizeProbPlot);
        plot.getRangeAxis().setRange(0.0, 1.0);
 
        // axis ticks interval
        //NB: this if commented out because it blocks automated selection of tick units
        // and therefore it allows ticks overlap when range is large
        //((NumberAxis) plot.getDomainAxis()).setTickUnit(new NumberTickUnit(1.0));
 
        // series line thickness
        XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
        renderer.setSeriesPaint(0, Color.decode("#db6d00"));
        renderer.setSeriesStroke(0, new BasicStroke(2.0f));
        plot.setRenderer(renderer);
 
        // font of axis label
        Font font3 = new Font("Dialog", Font.PLAIN, 12);
        plot.getDomainAxis().setLabelFont(font3);
        plot.getRangeAxis().setLabelFont(font3);
    }
    
//-----------------------------------------------------------------------------
 
    private void updateCrowdProbDataset() 
    {
        createCrowdProbDataset();
        ((XYPlot) graphCrowdProbJFChart.getPlot()).setDataset(crowdProbData);   
    }
        
//-----------------------------------------------------------------------------
 
    private void createCrowdProbDataset() 
    {   
        crowdProbData = new DefaultXYDataset();
        
        ArrayList<Double> y = new ArrayList<Double>();
        try
        {
            int scheme = GAParameters.convertProbabilityScheme(
                    cmbParCrowd1.getSelectedItem().toString());
            double l = (Double) spnParCrowd2.getValue();
            double s1 = (Double) spnParCrowd3.getValue();
            double s2 = (Double) spnParCrowd4.getValue();
            
            for (int crowdedness=0; crowdedness<100; crowdedness++)
            {
                double prob = EAUtils.getCrowdingProbabilityForCrowdedness(
                        crowdedness, scheme, l, s1, s2);
                y.add(prob);
            }
        }
        catch (Exception e)
        {
            e.printStackTrace();
            JOptionPane.showMessageDialog(this,
                    "<html>Exception occurred while reading mol growth "
                    + "proability scheme.<br>"
                    + "Please, report this to the DENOPTIM team.</html>",
                    "Error",
                    JOptionPane.ERROR_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
        }
 
        double[][] data = new double[2][y.size()];
        for (int crowdedness=0; crowdedness<100; crowdedness++)
        {
            data[0][crowdedness] = crowdedness;
            data[1][crowdedness] = y.get(crowdedness);
        }
        
        crowdProbData.addSeries("Crowding Probability", data);
    }
    
//-----------------------------------------------------------------------------
 
    private void createCrowdProbGraph() 
    {
        createCrowdProbDataset();
        createCrowdProbChart();
        graphCrowdProbJFChartChartPanel = new ChartPanel(graphCrowdProbJFChart);
        graphCrowdProbJFChartChartPanel.setMaximumSize(new Dimension(400,200));
    }
    
//-----------------------------------------------------------------------------
    
    private void createCrowdProbChart()
    {
        graphCrowdProbJFChart = ChartFactory.createXYLineChart(
            null,                         // plot title
            "Crowdedness",                // x axis label
            "Probability",                // y axis label
            crowdProbData,                 // data
            PlotOrientation.VERTICAL,  
            false,                        // include legend
            false,                        // tooltips
            false                         // urls
        );
 
        XYPlot plot = (XYPlot) graphCrowdProbJFChart.getPlot();
        
        // axis ranges
        plot.getDomainAxis().setRange(minLevelCrowdProbPlot, maxLevelCrowdProbPlot);
        plot.getRangeAxis().setRange(0.0, 1.0);
        
        // axis ticks interval 
        //NB: this if commented out because it blocks automated selection of tick units
        // and therefore it allows ticks overlap when range is large
        //((NumberAxis) plot.getDomainAxis()).setTickUnit(new NumberTickUnit(1.0));
 
        // series line thickness
        XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
        renderer.setSeriesPaint(0, Color.decode("#ff6db6"));
        renderer.setSeriesStroke(0, new BasicStroke(2.0f));
        plot.setRenderer(renderer);
        
        // font of axis label
        Font font3 = new Font("Dialog", Font.PLAIN, 12); 
        plot.getDomainAxis().setLabelFont(font3);
        plot.getRangeAxis().setLabelFont(font3);
    }
    
//-----------------------------------------------------------------------------
 
    @Override
    public void importParametersFromDenoptimParamsFile(String fileName) throws Exception
    {
        clearUnformattedTxtArea();
        checkedFlags.clear();
        checkedFlags.put(keyPar11, false);
        
        importParametersFromDenoptimParamsFile(fileName,"GA-");
 
        // We have also some fragmentation parameters in this form
        importParametersFromDenoptimParamsFile(fileName,"FRG-");
        
        rdbSrcOrNew.setSelected(false);
        localBlock1.setVisible(false);
        localBlock2.setVisible(true);
        switch (ProbabilityFuncitonShape.valueOf(
                cmbPar11.getSelectedItem().toString()))
        {
            case EXP_DIFF:
                localBlockLvlProb3.setVisible(true);
                localBlockLvlProb4.setVisible(false);   
                break;
                
            case TANH:
                localBlockLvlProb3.setVisible(true);
                localBlockLvlProb4.setVisible(false);   
                break;
                
            case SIGMA:
                localBlockLvlProb3.setVisible(false);
                localBlockLvlProb4.setVisible(true);   
                break;
                
            default:
                localBlockLvlProb3.setVisible(false);
                localBlockLvlProb4.setVisible(false);   
                break;
        }
        switch (ProbabilityFuncitonShape.valueOf(
                cmbParMolSz1.getSelectedItem().toString()))
        {
            case EXP_DIFF:
                localBlockMolSz3.setVisible(true);
                localBlockMolSz4.setVisible(false);
                break;
 
            case TANH:
                localBlockMolSz3.setVisible(true);
                localBlockMolSz4.setVisible(false);
                break;
 
            case SIGMA:
                localBlockMolSz3.setVisible(false);
                localBlockMolSz4.setVisible(true);
                break;
 
            default:
                localBlockMolSz3.setVisible(false);
                localBlockMolSz4.setVisible(false);
                break;
        }
        if (checkedFlags.get(keyPar11))
        {
            rbtLevelGrowth.setSelected(true);
            localBlockLvlProbAll.setVisible(true);
            localBlockMolSzAll.setVisible(false);
        } else {
            rbtMolSzGrowth.setSelected(true);
            localBlockLvlProbAll.setVisible(false);
            localBlockMolSzAll.setVisible(true);
        }
        
        switch (ProbabilityFuncitonShape.valueOf(
                cmbParCrowd1.getSelectedItem().toString()))
        {
            case EXP_DIFF:
                updateCrowdProbDataset();
                localBlockCrowd3.setVisible(true);
                localBlockCrowd4.setVisible(false);
                localBlockCrowdGraph.setVisible(true);
                break;
                
            case TANH:
                updateCrowdProbDataset();
                localBlockCrowd3.setVisible(true);
                localBlockCrowd4.setVisible(false);  
                localBlockCrowdGraph.setVisible(true);
                break;
                
            case SIGMA:
                updateCrowdProbDataset();
                localBlockCrowd3.setVisible(false);
                localBlockCrowd4.setVisible(true);
                localBlockCrowdGraph.setVisible(true);
                break;
                
            case UNRESTRICTED:
                updateCrowdProbDataset();
                localBlockCrowd3.setVisible(false);
                localBlockCrowd4.setVisible(false);
                localBlockCrowdGraph.setVisible(true);
                break;
                
            default:
                localBlockCrowd3.setVisible(false);
                localBlockCrowd4.setVisible(false); 
                localBlockCrowdGraph.setVisible(false);
                break;
        }
        
        advOptsBlock.setVisible(true);
        showUnknownKeyWarning(this, "Genetic Algorithm");
    }
 
//-----------------------------------------------------------------------------
    
    @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":
                ((JTextField) valueField).setText(value);
                break;
                
            case "class javax.swing.JRadioButton":
                ((JRadioButton) valueField).setSelected(true);
                break;
                
            case "class javax.swing.JComboBox":
                if (valueField==cmbParMolSz1 || valueField==cmbParCrowd1 ||
                       valueField==cmbPar11)
                {
                    ((JComboBox<ProbabilityFuncitonShape>) valueField)
                        .setSelectedItem(ProbabilityFuncitonShape.valueOf(
                                value.toUpperCase()));
                } else {
                    ((JComboBox<String>) valueField).setSelectedItem(
                            value.toUpperCase());
                }
                break;
                
            case "class javax.swing.table.DefaultTableModel":
 
                //WARNING: there might be cases where we do not take all the records
 
                ((DefaultTableModel) valueField).addRow(value.split(" "));
                break;
                
            case "class javax.swing.JSpinner":
 
                //WARNING: assuming all JSpinners work on doubles
                
                ((JSpinner) valueField).setValue(Double.parseDouble(value));
                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("# Genetic Algorithm - parameters").append(NL);
        
        if (rdbSrcOrNew.isSelected())
        {
            if (txtGASource.getText().equals("") || txtGASource.getText() == null)
            {
                throw new Exception("<html>No source specified for GA "
                        + "parameters.<br>Please, specify the file name.</html>");
            }
            importParametersFromDenoptimParamsFile(txtGASource.getText());
        }
        
        sb.append(getStringIfNotEmpty(keyPar3,txtPar3));
        sb.append(getStringIfNotEmpty(keyPar1,txtPar1));
        sb.append(keyPar2).append("=").append(cmbPar2.getSelectedItem())
        .append(NL);
        sb.append(getStringIfSelected(keyPar5,rdbPar5));
        sb.append(getStringIfSelected(keyPar5a,rdbPar5a));
        sb.append(getStringIfNotEmpty(keyPar6,txtPar6));
        sb.append(getStringIfNotEmpty(keyPar7,txtPar7));
        sb.append(getStringIfNotEmpty(keyPar8,txtPar8));
        sb.append(getStringIfNotEmpty(keyPar9,txtPar9));
        sb.append(getStringIfNotEmpty(keyPar10,txtPar10));
        if (rbtLevelGrowth.isSelected())
        {
            sb.append(keyPar11).append("=").append(cmbPar11.getSelectedItem())
            .append(NL);
            if (cmbPar11.getSelectedItem()!=ProbabilityFuncitonShape.UNRESTRICTED)
            {
                if (cmbPar11.getSelectedItem()==ProbabilityFuncitonShape.EXP_DIFF 
                        || cmbPar11.getSelectedItem()==ProbabilityFuncitonShape.TANH)
                {
                    sb.append(getStringForKVLine(keyPar12,spnPar12));
                } else if (cmbPar11.getSelectedItem()==ProbabilityFuncitonShape.SIGMA)
                {
                    sb.append(getStringForKVLine(keyPar13,spnPar13));
                    sb.append(getStringForKVLine(keyPar14,spnPar14));
                }
            }
        } else if (rbtMolSzGrowth.isSelected()) 
        {
            sb.append(keyParMolSz1).append("=")
            .append(cmbParMolSz1.getSelectedItem()).append(NL);
            if (cmbParMolSz1.getSelectedItem()!=ProbabilityFuncitonShape.UNRESTRICTED)
            {
                if (cmbParMolSz1.getSelectedItem()==ProbabilityFuncitonShape.EXP_DIFF 
                        || cmbParMolSz1.getSelectedItem()==ProbabilityFuncitonShape.TANH)
                {
                    sb.append(getStringForKVLine(keyParMolSz2,spnParMolSz2));
                } else if (cmbParMolSz1.getSelectedItem()==ProbabilityFuncitonShape.SIGMA)
                {
                    sb.append(getStringForKVLine(keyParMolSz3,spnParMolSz3));
                    sb.append(getStringForKVLine(keyParMolSz4,spnParMolSz4));
                }
            }
        }
        sb.append(keyParCrowd1).append("=")
        .append(cmbParCrowd1.getSelectedItem()).append(NL);
        if (cmbParCrowd1.getSelectedItem()!=ProbabilityFuncitonShape.UNRESTRICTED)
        {
            if (cmbParCrowd1.getSelectedItem()==ProbabilityFuncitonShape.EXP_DIFF 
                    || cmbParCrowd1.getSelectedItem()==ProbabilityFuncitonShape.TANH)
            {
                sb.append(getStringForKVLine(keyParCrowd2,spnParCrowd2));
            } else if (cmbParCrowd1.getSelectedItem()==ProbabilityFuncitonShape.SIGMA)
            {
                sb.append(getStringForKVLine(keyParCrowd3,spnParCrowd3));
                sb.append(getStringForKVLine(keyParCrowd4,spnParCrowd4));
            }
        }
        sb.append(keyPar15).append("=").append(cmbPar15.getSelectedItem())
        .append(NL);
        sb.append(getStringIfNotEmpty(keyPar16,txtPar16));
        sb.append(getStringIfNotEmpty(keyPar17,txtPar17));
        sb.append(getStringIfNotEmpty(keyParMSM,txtParMSM));
        sb.append(getStringIfNotEmpty(keyParWC,txtParWC));
        sb.append(getStringIfNotEmpty(keyPar18,txtPar18));
        sb.append(keyPar19).append("=").append(cmbPar19.getSelectedItem())
        .append(NL);
        
        sb.append(getStringIfNotEmpty(keyMolToGraph,txtMolToGraph));
        sb.append(getStringIfNotEmpty(keyFrgMols,txtFrgMols));
        sb.append(getStringIfSelected(keyAddH,rdbAddH));
        
        sb.append(getStringIfNotEmpty(keyPar20,txtPar20));
        sb.append(getStringIfNotEmpty(keyPar21,txtPar21));
        sb.append(getStringIfNotEmpty(keyPar22,txtPar22));
        sb.append(getStringIfNotEmpty(keyPar24,txtPar24));
        sb.append(keyPar25).append("=").append(cmbPar25.getSelectedItem())
        .append(NL);
        sb.append(getStringIfSelected(keyRingTmplsFrags,rdbRingTmplsFrags));
        sb.append(getStringIfSelected(keyRingTmplsScaff,rdbRingTmplsScaff));
        if (rdbRingTmplsScaff.isSelected() || rdbRingTmplsScaff.isSelected())
        {
            sb.append(getStringForKVLine(keyRingSysTmplTrhld,spnRingSysTmpl));
        }
        
        sb.append(getTextForUnformattedSettings()).append(NL);
        
        //HEREGOESPRINT this is only to facilitate automated insertion of code        
    }
}