FLASHDeconvHelperStructs.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Kyowon Jeong, Jihyung Kim $
// $Authors: Kyowon Jeong, Jihyung Kim $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h>
 
namespace OpenMS
{
  struct OPENMS_DLLAPI FLASHDeconvHelperStructs
  {
    class OPENMS_DLLAPI PrecalculatedAveragine
    {
    private:
      std::vector<IsotopeDistribution> isotopes_;
      std::vector<double> norms_;
      std::vector<double> average_mono_mass_difference_;
      std::vector<double> abundant_mono_mass_difference_;
      std::vector<int> left_count_from_apex_;
      std::vector<int> right_count_from_apex_;
      std::vector<Size> apex_index_;
 
      Size max_isotope_index_;
      double mass_interval_;
      double min_mass_;
      Size massToIndex_(double mass) const;
    public:
      PrecalculatedAveragine() = default;
 
      PrecalculatedAveragine(double min_mass,
                             double max_mass,
                             double delta,
                             CoarseIsotopePatternGenerator &generator,
                             bool use_RNA_averagine);
 
 
      PrecalculatedAveragine(const PrecalculatedAveragine& ) = default;
 
      PrecalculatedAveragine(PrecalculatedAveragine&& other) noexcept = default;
 
      PrecalculatedAveragine& operator=(const PrecalculatedAveragine& pc) = default;
 
      PrecalculatedAveragine& operator=(PrecalculatedAveragine&& pc) noexcept = default;
 
      ~PrecalculatedAveragine() = default ;
 
 
      IsotopeDistribution get(double mass) const;
 
      size_t getMaxIsotopeIndex() const;
 
      void setMaxIsotopeIndex(int index);
 
      Size getLeftCountFromApex(double mass) const;
 
      Size getRightCountFromApex(double mass) const;
 
      Size getApexIndex(double mass) const;
 
      Size getLastIndex(double mass) const;
 
      double getAverageMassDelta(double mass) const;
 
      double getMostAbundantMassDelta(double mass) const;
    };
 
    struct OPENMS_DLLAPI MassFeature
    {
    public:
      MassTrace mt;
      std::vector<float> per_charge_intensity;
      std::vector<float> per_isotope_intensity;
      int iso_offset;
      int scan_number, rep_charge;
      double avg_mass;
      int min_charge, max_charge, charge_count;
      double isotope_score, qscore;
      double rep_mz;
    };
 
    class OPENMS_DLLAPI LogMzPeak
    {
    public:
      double mz = 0;
      float intensity = 0;
      double logMz = -1000;
      double mass = .0;
      int abs_charge = 0;
      bool is_positive = true;
      int isotopeIndex = -1;
 
      LogMzPeak() = default;
 
      explicit LogMzPeak(const Peak1D& peak, bool positive);
 
      LogMzPeak(const LogMzPeak& ) = default;
 
      ~LogMzPeak() = default;
 
      double getUnchargedMass();
 
      bool operator<(const LogMzPeak& a) const;
      bool operator>(const LogMzPeak& a) const;
      bool operator==(const LogMzPeak& other) const;
    };
 
    static double getLogMz(double mz, bool positive);
 
    static float getChargeMass(bool positive_ioniziation_mode);
  };
}