OfflinePrecursorIonSelection.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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/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_;
  };
 
}