DIAHelper.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: Hannes Roest $
// $Authors: Witold Wolski, Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
 
#include <vector>
 
namespace OpenMS
{
  class TheoreticalSpectrumGenerator;
  namespace DIAHelpers
  {
 
 
    OPENMS_DLLAPI bool integrateWindow(const OpenSwath::SpectrumPtr& spectrum, double mz_start,
                                       double mz_end, double& mz, double& intensity, bool centroided = false);
 
    OPENMS_DLLAPI void integrateWindows(const OpenSwath::SpectrumPtr& spectrum, 
                                        const std::vector<double>& windows_center, 
                                        double width,
                                        std::vector<double>& integrated_windows_intensity,
                                        std::vector<double>& integrated_windows_mz,
                                        bool remove_zero = false);
 
    OPENMS_DLLAPI void integrateDriftSpectrum(const OpenSwath::SpectrumPtr& spectrum,
                                              double mz_start,
                                              double mz_end,
                                              double & im,
                                              double & intensity,
                                              double drift_start,
                                              double drift_end);
 
    OPENMS_DLLAPI void adjustExtractionWindow(double& right, double& left, const double& mz_extract_window, const bool& mz_extraction_ppm);
 
    OPENMS_DLLAPI void getBYSeries(const AASequence& a,
                                   std::vector<double>& bseries,
                                   std::vector<double>& yseries,
                                   TheoreticalSpectrumGenerator const * g,
                                   int charge = 1);
 
    OPENMS_DLLAPI void getTheorMasses(const AASequence& a,
                                      std::vector<double>& masses,
                                      TheoreticalSpectrumGenerator const * g,
                                      int charge = 1);
 
    OPENMS_DLLAPI void getAveragineIsotopeDistribution(const double product_mz,
                                         std::vector<std::pair<double, double> >& isotopes_spec,
                                         const int charge = 1,
                                         const int nr_isotopes = 4,
                                         const double mannmass = 1.00048);
 
    OPENMS_DLLAPI void simulateSpectrumFromAASequence(const AASequence& aa,
                                        std::vector<double>& first_isotope_masses, //[out]
                                        std::vector<std::pair<double, double> >& isotope_masses, //[out]
                                        TheoreticalSpectrumGenerator const * g,
                                        int charge = 1);
 
    OPENMS_DLLAPI void modifyMassesByCharge(const std::vector<std::pair<double, double> >& masses, 
                              std::vector<std::pair<double, double> >& modmass, 
                              int charge = 1);
 
    OPENMS_DLLAPI void addPreisotopeWeights(const std::vector<double>& first_isotope_masses,
                              std::vector<std::pair<double, double> >& isotope_spec, // output
                              UInt nr_peaks = 2, //nr of pre-isotope peaks
                              double pre_isotope_peaks_weight = -0.5, // weight of pre-isotope peaks
                              double mannmass = 1.000482, //
                              int charge = 1);
 
    OPENMS_DLLAPI void addPreisotopeWeights(double mz,
                                            std::vector<std::pair<double, double> >& isotope_spec, // output
                                            UInt nr_peaks = 2, //nr of pre-isotope peaks
                                            double pre_isotope_peaks_weight = -0.5, // weight of pre-isotope peaks
                                            double mannmass = 1.000482, //
                                            int charge = 1);
 
    OPENMS_DLLAPI void addIsotopes2Spec(const std::vector<std::pair<double, double> >& spec,
                          std::vector<std::pair<double, double> >& isotope_masses, //[out]
                          Size nr_isotopes, int charge = 1);
 
    OPENMS_DLLAPI void addSinglePeakIsotopes2Spec(double mz, double ity,
                                                  std::vector<std::pair<double, double> >& isotope_masses, //[out]
                                                  Size nr_isotopes, int charge);
 
    OPENMS_DLLAPI void sortByFirst(std::vector<std::pair<double, double> >& tmp);
    OPENMS_DLLAPI void extractFirst(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
    OPENMS_DLLAPI void extractSecond(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
    
  }
}