de.unijena.bioinf.IsotopePatternAnalysis.scoring.LogNormDistributedIntensityScorer.java Source code

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Here is the source code for de.unijena.bioinf.IsotopePatternAnalysis.scoring.LogNormDistributedIntensityScorer.java

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/*
 *  This file is part of the SIRIUS library for analyzing MS and MS/MS data
 *
 *  Copyright (C) 2013-2015 Kai Dhrkop
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; either
 *  version 2.1 of the License, or (at your option) any later version.
 *
 *  This library 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
 *  Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License along with SIRIUS.  If not, see <http://www.gnu.org/licenses/>.
 */
package de.unijena.bioinf.IsotopePatternAnalysis.scoring;

import de.unijena.bioinf.ChemistryBase.algorithm.ParameterHelper;
import de.unijena.bioinf.ChemistryBase.data.DataDocument;
import de.unijena.bioinf.ChemistryBase.ms.*;
import de.unijena.bioinf.ChemistryBase.ms.utils.SimpleMutableSpectrum;
import de.unijena.bioinf.ChemistryBase.ms.utils.Spectrums;
import de.unijena.bioinf.IsotopePatternAnalysis.util.IntensityDependency;
import de.unijena.bioinf.IsotopePatternAnalysis.util.LinearIntensityDependency;
import org.apache.commons.math3.special.Erf;

import static java.lang.Math.*;

public class LogNormDistributedIntensityScorer implements IsotopePatternScorer {

    private final static double root2 = sqrt(2d);

    private IntensityDependency intensityDependency;

    public LogNormDistributedIntensityScorer(IntensityDependency intensityDependency) {
        this.intensityDependency = intensityDependency;
    }

    public LogNormDistributedIntensityScorer(double fullIntensityPrecision, double minIntensityPrecision) {
        this(new LinearIntensityDependency(fullIntensityPrecision, minIntensityPrecision));
    }

    public LogNormDistributedIntensityScorer() {
        this(0.1, 0.9);
    }

    @Override
    public double score(Spectrum<Peak> measuredSpectrum, Spectrum<Peak> theoreticalPattern, Normalization norm,
            Ms2Experiment experiment, MeasurementProfile profile) {
        // remove peaks from theoretical pattern until the length of both spectra is equal
        final MutableSpectrum<Peak> theoreticalSpectrum = new SimpleMutableSpectrum(theoreticalPattern);
        while (measuredSpectrum.size() < theoreticalSpectrum.size()) {
            theoreticalSpectrum.removePeakAt(theoreticalSpectrum.size() - 1);
        }
        // re-normalize
        Spectrums.normalize(theoreticalSpectrum, norm);
        // score
        double score = 0d;
        final double intensityDeviation = profile.getIntensityDeviation();
        for (int i = 0; i < measuredSpectrum.size(); ++i) {
            final double intensity = measuredSpectrum.getIntensityAt(i);
            final double thIntensity = theoreticalSpectrum.getIntensityAt(i);
            // TODO: TEST!!!!!!!!!!!
            final double sd = Math.abs(log(intensity)
                    - log(intensity + intensityDeviation * intensityDependency.getValueAt(intensity)));//log(1 + intensityDeviation*intensityDependency.getValueAt(intensity));
            final double newScore = log(Erf.erfc(abs(log(thIntensity / intensity) / (root2 * sd))));
            if (Double.isInfinite(newScore))
                return newScore;
            score += newScore;
        }
        return score;
    }

    @Override
    public <G, D, L> void importParameters(ParameterHelper helper, DataDocument<G, D, L> document, D dictionary) {
        this.intensityDependency = (IntensityDependency) helper.unwrap(document,
                document.getFromDictionary(dictionary, "intensityDependency"));
    }

    @Override
    public <G, D, L> void exportParameters(ParameterHelper helper, DataDocument<G, D, L> document, D dictionary) {
        document.addToDictionary(dictionary, "intensityDependency", helper.wrap(document, intensityDependency));
    }
}