overlaps.h

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/* overlaps.h :  Mass spectrum Overlap finding algorithms
 * 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_OVERLAPS_H
#define ATOMPROBE_OVERLAPS_H

#include "atomprobe/isotopes/abundance.h"
#include "atomprobe/helper/stringFuncs.h"
#include "atomprobe/io/ranges.h"

#include <utility>
#include <set>

namespace AtomProbe
{


void findOverlaps(const AbundanceData &natData,
            const RangeFile &rng, float massDelta, unsigned int maxCharge,
            std::vector<std::pair< size_t,size_t> > &overlapIdx, std::vector<std::pair<float,float> > &overlapMasses );

void findOverlaps(const AbundanceData &natData,
            const std::vector<std::string> &ions, float massDelta, unsigned int maxCharge,
            std::vector<std::pair< size_t,size_t> > &overlapIdx, std::vector<std::pair<float,float> > &overlapMasses );


// - massDistributions is a vector of isotope fingerprints, where the first entry in the pair is mass and the second (unused) is intensity
// - skipIds (optional - can be empty) are the IDs of mass distributions to ignore
void findOverlapsFromSpectra(const std::vector<std::vector<std::pair<float,float> > > &massDistributions,
            float massDelta,const std::set<unsigned int> &skipIDs,
            std::vector<std::pair<size_t ,size_t> > &overlapIdx,
            std::vector<std::pair<float,float> > &overlapMasses);
#ifdef DEBUG
bool testOverlapDetect();
#endif

}
#endif