guineu.modules.dataanalysis.variationCoefficientRow.variationCoefficientRowFilterTask.java Source code

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Here is the source code for guineu.modules.dataanalysis.variationCoefficientRow.variationCoefficientRowFilterTask.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.variationCoefficientRow;

import guineu.data.Dataset;
import guineu.data.PeakListRow;
import guineu.taskcontrol.AbstractTask;
import guineu.taskcontrol.TaskStatus;
import guineu.util.GUIUtils;
import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;

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

    private Dataset[] datasets;
    private double progress;

    public variationCoefficientRowFilterTask(Dataset[] datasets) {
        this.datasets = datasets;

    }

    public String getTaskDescription() {
        return "std Dev scores... ";
    }

    public double getFinishedPercentage() {
        return progress;
    }

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

    public void run() {
        try {
            setStatus(TaskStatus.PROCESSING);
            this.variationCoefficient();
            setStatus(TaskStatus.FINISHED);
        } catch (Exception e) {
            setStatus(TaskStatus.ERROR);
            errorMessage = e.toString();
            return;
        }
    }

    public void variationCoefficient() {
        progress = 0.0f;
        double steps = 1f / datasets.length;
        for (Dataset dataset : datasets) {
            Dataset newDataset = dataset.clone();
            newDataset.setDatasetName("Var Coefficient - " + dataset.getDatasetName());
            newDataset.addColumnName("Coefficient of variation");
            for (PeakListRow lipid : newDataset.getRows()) {
                double stdDev = this.CoefficientOfVariation(lipid);
                lipid.setPeak("Coefficient of variation", stdDev);
            }
            progress += steps;
            progress = 0.5f;
            GUIUtils.showNewTable(newDataset, true);
        }
        progress = 1f;

    }

    public double CoefficientOfVariation(PeakListRow row) {
        DescriptiveStatistics stats = new DescriptiveStatistics();
        for (Object peak : row.getPeaks(null)) {
            if (peak != null) {
                stats.addValue((Double) peak);
            }
        }
        return stats.getStandardDeviation() / stats.getMean();
    }
}