guineu.modules.filter.Alignment.centering.mean.MeanCenteringTask.java Source code

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Here is the source code for guineu.modules.filter.Alignment.centering.mean.MeanCenteringTask.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.filter.Alignment.centering.mean;

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

class MeanCenteringTask extends AbstractTask {

    private Dataset peakLists[];
    // Processed rows counter
    private int processedRows, totalRows;

    public MeanCenteringTask(Dataset[] peakLists) {

        this.peakLists = peakLists;
    }

    public String getTaskDescription() {
        return "Mean centering";
    }

    public double getFinishedPercentage() {
        if (totalRows == 0) {
            return 0f;
        }
        return (double) processedRows / (double) totalRows;
    }

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

    /**
     * @see Runnable#run()
     */
    public void run() {
        setStatus(TaskStatus.PROCESSING);

        for (Dataset data : this.peakLists) {
            normalize(data);
        }
        setStatus(TaskStatus.FINISHED);

    }

    private void normalize(Dataset data) {
        DescriptiveStatistics stats = new DescriptiveStatistics();
        for (String nameExperiment : data.getAllColumnNames()) {
            for (PeakListRow row : data.getRows()) {
                Object value = row.getPeak(nameExperiment);
                if (value != null && value instanceof Double) {
                    stats.addValue((Double) value);
                }
            }
            for (PeakListRow row : data.getRows()) {
                Object value = row.getPeak(nameExperiment);
                if (value != null && value instanceof Double) {
                    row.setPeak(nameExperiment, Math.abs((Double) value - stats.getMean()));
                }
            }
            stats.clear();
        }
    }
}