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 2002-2018.
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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);

    };

  };
}