guineu.modules.dataanalysis.foldChanges.FoldTestTask.java Source code

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Here is the source code for guineu.modules.dataanalysis.foldChanges.FoldTestTask.java

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/*
 * Copyright 2007-2013 VTT Biotechnology
 * This file is part of Guineu.
 *
 * Guineu is free software; you can redistribute it and/or modify it under the
 * terms of the GNU General Public License as published by the Free Software
 * Foundation; either version 2 of the License, or (at your option) any later
 * version.
 *
 * Guineu 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License along with
 * Guineu; if not, write to the Free Software Foundation, Inc., 51 Franklin St,
 * Fifth Floor, Boston, MA 02110-1301 USA
 */
package guineu.modules.dataanalysis.foldChanges;

import guineu.data.Dataset;
import guineu.data.PeakListRow;
import guineu.taskcontrol.AbstractTask;
import guineu.taskcontrol.TaskStatus;
import guineu.util.GUIUtils;
import guineu.util.components.FileUtils;
import java.util.List;
import org.apache.commons.math.MathException;
import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;

/**
 *
 * @author scsandra
 */
public class FoldTestTask extends AbstractTask {

    private double progress = 0.0f;
    private Dataset dataset;
    private String parameter;

    public FoldTestTask(Dataset dataset, FoldTestParameters parameters) {
        this.dataset = dataset;
        this.parameter = parameters.getParameter(FoldTestParameters.groups).getValue();
    }

    @Override
    public String getTaskDescription() {
        return "Fold Changes... ";
    }

    @Override
    public double getFinishedPercentage() {
        return progress;
    }

    @Override
    public void cancel() {
        setStatus(TaskStatus.CANCELED);
    }

    @Override
    public void run() {
        try {
            setStatus(TaskStatus.PROCESSING);
            double[] t = new double[dataset.getNumberRows()];
            for (int i = 0; i < dataset.getNumberRows(); i++) {
                t[i] = this.Foldtest(i);
            }

            Dataset newDataset = FileUtils.getDataset(dataset, "Fold changes - ");
            progress = 0.3f;
            newDataset.addColumnName("Fold changes");
            int cont = 0;
            for (PeakListRow row : dataset.getRows()) {
                PeakListRow newRow = row.clone();
                newRow.setPeak("Fold changes", t[cont++]);
                newDataset.addRow(newRow);
            }
            progress = 0.5f;

            GUIUtils.showNewTable(newDataset, true);

            progress = 1f;
            setStatus(TaskStatus.FINISHED);

        } catch (Exception e) {
            setStatus(TaskStatus.ERROR);
            errorMessage = e.toString();
        }
    }

    public double Foldtest(int mol) throws IllegalArgumentException, MathException {
        DescriptiveStatistics stats1 = new DescriptiveStatistics();
        DescriptiveStatistics stats2 = new DescriptiveStatistics();

        String parameter1 = "";

        try {
            // Determine groups for selected raw data files
            List<String> availableParameterValues = dataset.getParameterAvailableValues(parameter);

            int numberOfGroups = availableParameterValues.size();

            if (numberOfGroups > 1) {
                parameter1 = availableParameterValues.get(0);
                String parameter2 = availableParameterValues.get(1);

                for (String sampleName : dataset.getAllColumnNames()) {
                    if (dataset.getParametersValue(sampleName, parameter) != null
                            && dataset.getParametersValue(sampleName, parameter).equals(parameter1)) {
                        stats1.addValue((Double) this.dataset.getRow(mol).getPeak(sampleName));
                    } else if (dataset.getParametersValue(sampleName, parameter) != null
                            && dataset.getParametersValue(sampleName, parameter).equals(parameter2)) {
                        stats2.addValue((Double) this.dataset.getRow(mol).getPeak(sampleName));
                    }
                }
            } else {
                return -1;
            }

        } catch (Exception e) {
            e.printStackTrace();
        }

        if (stats1.getN() > 0 && stats2.getN() > 0) {
            /*double[] sortValues1 = stats1.getSortedValues();
             double[] sortValues2 = stats2.getSortedValues();
                
             return sortValues1[((int) stats1.getN() / 2)] / sortValues2[((int) stats2.getN() / 2)];*/
            return stats1.getMean() / stats2.getMean();
        } else {
            return 0;
        }
    }
}