// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
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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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// $Maintainer: Hannes Roest $
// $Authors: Witold Wolski, Hannes Roest $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_OPENSWATH_DIAHELPER_H
#define OPENMS_ANALYSIS_OPENSWATH_DIAHELPER_H

#include <vector>
#include <OpenMS/CHEMISTRY/AASequence.h>

namespace OpenMS
{
  namespace DIAHelpers
  {
    /**
      @brief Helper functions for the DIA scoring of OpenSWATH
    */
    ///@{
    /// compute the b and y series masses for a given AASequence
    OPENMS_DLLAPI void getBYSeries(AASequence& a,
                     std::vector<double>& bseries, std::vector<double>& yseries, UInt charge = 1u);

    /// for SWATH -- get the theoretical b and y series masses for a sequence
    OPENMS_DLLAPI void getTheorMasses(AASequence& a, std::vector<double>& masses, UInt charge = 1u);

    /// get averagine distribution given mass
    OPENMS_DLLAPI void getAveragineIsotopeDistribution(double product_mz,
                                         std::vector<std::pair<double, double> >& isotopesSpec, 
                                         double charge = 1.,
                                         int nr_isotopes = 4,
                                         double mannmass = 1.00048);

    /// simulate spectrum from AASequence
    OPENMS_DLLAPI void simulateSpectrumFromAASequence(AASequence& aa,
                                        std::vector<double>& firstIsotopeMasses, //[out]
                                        std::vector<std::pair<double, double> >& isotopeMasses, //[out]
                                        double charge = 1.);

    /// modify masses by charge
    OPENMS_DLLAPI void modifyMassesByCharge(const std::vector<std::pair<double, double> >& masses, //![in]
                              std::vector<std::pair<double, double> >& modmass, //!< [out]
                              double charge = 1.);

    /// add negative pre-isotope weights to spectrum
    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.);

    /// given an experimental spectrum add isotope pattern.
    OPENMS_DLLAPI void addIsotopes2Spec(const std::vector<std::pair<double, double> >& spec,
                          std::vector<std::pair<double, double> >& isotopeMasses, //[out]
                          double charge = 1.);

    /// sorts vector of pairs by first
    OPENMS_DLLAPI void sortByFirst(std::vector<std::pair<double, double> >& tmp);
    /// extract first from vector of pairs
    OPENMS_DLLAPI void extractFirst(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
    /// extract second from vector of pairs
    OPENMS_DLLAPI void extractSecond(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
    
    ///}@
  }
}
#endif
