DIAHelper.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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// For a full list of authors, refer to the file AUTHORS.
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// $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(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,
                                   UInt charge = 1u);
 
    OPENMS_DLLAPI void getTheorMasses(const AASequence& a,
                                      std::vector<double>& masses,
                                      TheoreticalSpectrumGenerator const * g,
                                      UInt charge = 1u);
 
    OPENMS_DLLAPI void getAveragineIsotopeDistribution(const double product_mz,
                                         std::vector<std::pair<double, double> >& isotopesSpec,
                                         const double charge = 1.,
                                         const int nr_isotopes = 4,
                                         const double mannmass = 1.00048);
 
    OPENMS_DLLAPI void simulateSpectrumFromAASequence(const AASequence& aa,
                                        std::vector<double>& firstIsotopeMasses, //[out]
                                        std::vector<std::pair<double, double> >& isotopeMasses, //[out]
                                        TheoreticalSpectrumGenerator const * g,
                                        double charge = 1.);
 
    OPENMS_DLLAPI void modifyMassesByCharge(const std::vector<std::pair<double, double> >& masses, 
                              std::vector<std::pair<double, double> >& modmass, 
                              double charge = 1.);
 
    OPENMS_DLLAPI void addPreisotopeWeights(const std::vector<double>& firstIsotopeMasses,
                              std::vector<std::pair<double, double> >& isotopeSpec, // output
                              UInt nrpeaks = 2, //nr of pre-isotope peaks
                              double preIsotopePeaksWeight = -0.5, // weight of pre-isotope peaks
                              double mannmass = 1.000482, //
                              double charge = 1.);
 
    OPENMS_DLLAPI void addIsotopes2Spec(const std::vector<std::pair<double, double> >& spec,
                          std::vector<std::pair<double, double> >& isotopeMasses, //[out]
                          double charge = 1.);
 
    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);
    
  }
}