MultiplexClustering.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Lars Nilse $
// $Authors: Lars Nilse $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/MATH/MISC/BSpline2d.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredMSExperiment.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFiltering.h>
#include <OpenMS/COMPARISON/CLUSTERING/GridBasedCluster.h>
 
#include <vector>
#include <algorithm>
#include <iostream>
 
namespace OpenMS
{
    class OPENMS_DLLAPI MultiplexClustering :
        public ProgressLogger
    {        
        public:
        typedef GridBasedCluster::Point Point;    
 
        MultiplexClustering(const MSExperiment& exp_profile, const MSExperiment& exp_picked, const std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& boundaries, double rt_typical);
        
        MultiplexClustering(const MSExperiment& exp, double mz_tolerance, bool mz_tolerance_unit, double rt_typical);
        
        std::vector<std::map<int,GridBasedCluster> > cluster(const std::vector<MultiplexFilteredMSExperiment>& filter_results);
        
        class OPENMS_DLLAPI MultiplexDistance
        {
            public:
            MultiplexDistance(double rt_scaling);
       
            MultiplexDistance();
            
            double operator()(const Point& p1, const Point& p2) const;
     
            private:
            double rt_scaling_;
            
        };
 
        private:
        std::vector<double> grid_spacing_mz_;
        std::vector<double> grid_spacing_rt_;
                
        double rt_scaling_;
        
        double rt_typical_;
        
        //unused
        //double rt_minimum_;
        
   };
  
}