FeatureFinderAlgorithmPickedHelperStructs.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.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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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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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Stephan Aiche $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Exception.h>
 
#include <OpenMS/DATASTRUCTURES/ConvexHull2D.h>
#include <OpenMS/KERNEL/Peak1D.h>
 
#include <vector>
#include <list>
#include <cmath>
 
namespace OpenMS
{
 
  struct OPENMS_DLLAPI FeatureFinderAlgorithmPickedHelperStructs
  {
 
    struct OPENMS_DLLAPI Seed
    {
      Size spectrum;
      Size peak;
      float intensity;
 
      bool operator<(const Seed& rhs) const;
 
    };
 
    struct OPENMS_DLLAPI MassTrace
    {
      const Peak1D* max_peak;
      double max_rt;
 
      double theoretical_int;
 
      std::vector<std::pair<double, const Peak1D*> > peaks;
 
      ConvexHull2D getConvexhull() const;
 
      void updateMaximum();
 
      double getAvgMZ() const;
 
      bool isValid() const;
 
    };
 
    struct OPENMS_DLLAPI MassTraces :
      private std::vector<MassTrace>
    {
      typedef std::vector<MassTrace> privvec;
 
      // public exports of used methods
      using privvec::size;
      using privvec::at;
      using privvec::reserve;
      using privvec::push_back;
      using privvec::operator[];
      using privvec::back;
      using privvec::clear;
      using privvec::begin;
      using privvec::end;
      typedef privvec::iterator iterator;
      typedef privvec::const_iterator const_iterator;
 
      MassTraces();
 
      Size getPeakCount() const;
 
      bool isValid(double seed_mz, double trace_tolerance);
 
      Size getTheoreticalmaxPosition() const;
 
      void updateBaseline();
 
      std::pair<double, double> getRTBounds() const;
 
      void computeIntensityProfile(std::list<std::pair<double, double> >& intensity_profile) const;
 
      Size max_trace;
      double baseline;
    };
 
    struct OPENMS_DLLAPI TheoreticalIsotopePattern
    {
      std::vector<double> intensity;
      Size optional_begin;
      Size optional_end;
      double max;
      Size trimmed_left;
      Size size() const;
 
    };
 
    struct OPENMS_DLLAPI IsotopePattern
    {
      std::vector<SignedSize> peak;
      std::vector<Size> spectrum;
      std::vector<double> intensity;
      std::vector<double> mz_score;
      std::vector<double> theoretical_mz;
      TheoreticalIsotopePattern theoretical_pattern;
 
      explicit IsotopePattern(Size size);
 
    };
 
  };
}