guineu.modules.dataanalysis.zeroImputation.ZeroImputationTask.java Source code

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Here is the source code for guineu.modules.dataanalysis.zeroImputation.ZeroImputationTask.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.zeroImputation;

import guineu.data.Dataset;
import guineu.data.PeakListRow;
import guineu.taskcontrol.AbstractTask;
import guineu.taskcontrol.TaskStatus;
import java.util.List;
import org.apache.commons.math.random.RandomDataImpl;

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

    private Dataset dataset;
    private double progress;
    private RandomDataImpl data;

    public ZeroImputationTask(Dataset dataset) {
        this.dataset = dataset;
        data = new RandomDataImpl();
    }

    @Override
    public String getTaskDescription() {
        return "Zero imputation... ";
    }

    public double getFinishedPercentage() {
        return progress;
    }

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

    public void run() {
        try {
            setStatus(TaskStatus.PROCESSING);
            for (PeakListRow row : dataset.getRows()) {
                double min = getMinimun(row, dataset.getAllColumnNames());
                double zeroVal = min * 0.5;
                for (String name : dataset.getAllColumnNames()) {
                    // double randomVal = data.nextGaussian(zeroVal, 0.5);
                    Double peak = (Double) row.getPeak(name);
                    if (peak == 0) {
                        row.setPeak(name, Math.abs(zeroVal));
                    }
                }
            }

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

    private double getMinimun(PeakListRow row, List<String> columnName) {
        double min = Double.MAX_VALUE;
        for (String name : columnName) {
            double value = (Double) row.getPeak(name);
            if (value > 0 && value < min) {
                min = value;
            }
        }
        return min;
    }
}