filter.h

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/* filter.h: mass spectrum candidate filtering
 * Copyright (C) 2020  Daniel Haley
 * 
 * This program 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 3 of the License, or
 * (at your option) any later version.
 * 
 * This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
 */
#ifndef ATOMPROBE_MASS__FILTER_H
#define ATOMPROBE_MASS__FILTER_H

#include <vector>
#include <utility>

#include "atomprobe/isotopes/abundance.h"
#include "atomprobe/algorithm/massTool.h"

namespace AtomProbe
{


void filterPeakNeedBiggerObs(const AtomProbe::AbundanceData &massTable,
                const std::vector<float> &peakData, float tolerance,
                size_t solutionCharge, std::vector<std::vector<AtomProbe::ISOTOPE_ENTRY> > &solutions);



void filterBySolutionPPM(const AtomProbe::AbundanceData &massTable, 
        float minPpm, std::vector<std::vector<AtomProbe::ISOTOPE_ENTRY> > &solutions);


std::vector<float> maxExplainedFraction(const std::vector<std::pair<float,float> > &massData, 
    float peakMass, float massWidth, const std::vector<std::vector<AtomProbe::ISOTOPE_ENTRY> > &solutions, 
            const AtomProbe::AbundanceData &massTable, float massDistTol, unsigned int solutionCharge);
#ifdef DEBUG
    bool isotopeFilterTests();
#endif
}
#endif