OfflinePrecursorIonSelection.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
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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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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Alexandra Zerck $
// --------------------------------------------------------------------------

#pragma once


#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/ANALYSIS/ID/IDMapper.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/ANALYSIS/TARGETED/PSLPFormulation.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>

namespace OpenMS
{
  class PeptideIdentification;
  class ProteinIdentification;
  class String;


  class OPENMS_DLLAPI OfflinePrecursorIonSelection :
    public DefaultParamHandler
  {
public:
    typedef PSLPFormulation::IndexTriple IndexTriple;

    OfflinePrecursorIonSelection();
    ~OfflinePrecursorIonSelection() override;

    void makePrecursorSelectionForKnownLCMSMap(const FeatureMap& features,
                                               const PeakMap& experiment,
                                               PeakMap& ms2,
                                               std::set<Int>& charges_set,
                                               bool feature_based);

    void getMassRanges(const FeatureMap& features,
                       const PeakMap& experiment,
                       std::vector<std::vector<std::pair<Size, Size> > >& indices);

    void createProteinSequenceBasedLPInclusionList(String include, String rt_model_file, String pt_model_file, FeatureMap& precursors);

    void setLPSolver(LPWrapper::SOLVER solver)
    {
      solver_ = solver;
      std::cout << " LPSolver set to " << solver_ << std::endl;
    }

    LPWrapper::SOLVER getLPSolver()
    {
      return solver_;
    }

private:

    template <typename PairType>
    struct PairComparatorSecondElement
    {
      bool operator()(const PairType & left, const PairType & right) const
      {
        return left.second < right.second;
      }

    };

    typedef std::map<std::pair<double, double>, int, PairComparatorSecondElement<std::pair<double, double> > > ExclusionListType_;

    void calculateXICs_(const FeatureMap& features,
                        const std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
                        const PeakMap& experiment,
                        const std::set<Int>& charges_set,
                        std::vector<std::vector<std::pair<Size, double> > >& xics);

    void checkMassRanges_(std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
                          const PeakMap& experiment);

    void updateExclusionList_(ExclusionListType_& exclusion_list) const;

    LPWrapper::SOLVER solver_;
  };
 
}