MSChromatogram.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/StandardDeclarations.h>
#include <OpenMS/METADATA/ChromatogramSettings.h>
#include <OpenMS/METADATA/MetaInfoDescription.h>
#include <OpenMS/KERNEL/RangeManager.h>
#include <OpenMS/KERNEL/ChromatogramPeak.h>
#include <OpenMS/METADATA/DataArrays.h>

namespace OpenMS
{
  class ChromatogramPeak;

  class OPENMS_DLLAPI MSChromatogram :
    private std::vector<ChromatogramPeak>,
    public RangeManagerContainer<RangeRT, RangeIntensity>,
    public ChromatogramSettings
  {

public:

    struct OPENMS_DLLAPI MZLess
    {
      bool operator()(const MSChromatogram& a, const MSChromatogram& b) const;
    };

    typedef ChromatogramPeak PeakType;
    typedef typename PeakType::CoordinateType CoordinateType;
    typedef std::vector<PeakType> ContainerType;
    typedef RangeManager<RangeRT, RangeIntensity> RangeManagerType;
    typedef OpenMS::DataArrays::FloatDataArray FloatDataArray ;
    typedef std::vector<FloatDataArray> FloatDataArrays;
    typedef OpenMS::DataArrays::StringDataArray StringDataArray ;
    typedef std::vector<StringDataArray> StringDataArrays;
    typedef OpenMS::DataArrays::IntegerDataArray IntegerDataArray ;
    typedef std::vector<IntegerDataArray> IntegerDataArrays;


    typedef typename ContainerType::iterator Iterator;
    typedef typename ContainerType::const_iterator ConstIterator;
    typedef typename ContainerType::reverse_iterator ReverseIterator;
    typedef typename ContainerType::const_reverse_iterator ConstReverseIterator;


    using ContainerType::operator[];
    using ContainerType::begin;
    using ContainerType::cbegin;
    using ContainerType::rbegin;
    using ContainerType::end;
    using ContainerType::cend;
    using ContainerType::rend;
    using ContainerType::resize;
    using ContainerType::size;
    using ContainerType::push_back;
    using ContainerType::pop_back;
    using ContainerType::empty;
    using ContainerType::front;
    using ContainerType::back;
    using ContainerType::reserve;
    using ContainerType::insert;
    using ContainerType::erase;
    using ContainerType::swap;

    using typename ContainerType::iterator;
    using typename ContainerType::const_iterator;
    using typename ContainerType::size_type;
    using typename ContainerType::value_type;
    using typename ContainerType::reference;
    using typename ContainerType::const_reference;
    using typename ContainerType::pointer;
    using typename ContainerType::difference_type;

    MSChromatogram() = default;

    MSChromatogram(const MSChromatogram&) = default;

    MSChromatogram(MSChromatogram&&) = default;

    ~MSChromatogram() = default;

    MSChromatogram& operator=(const MSChromatogram& source);

    MSChromatogram& operator=(MSChromatogram&&) & = default;

    bool operator==(const MSChromatogram& rhs) const;

    bool operator!=(const MSChromatogram& rhs) const
    {
      return !(operator==(rhs));
    }

    // Docu in base class (RangeManager)
    void updateRanges() override
    {
      clearRanges();
      for (const auto& peak : (ContainerType&) *this)
      {
        extendRT(peak.getRT());
        extendIntensity(peak.getIntensity());
      }
    }

    const String& getName() const;

    void setName(const String& name);


    double getMZ() const;

    const FloatDataArrays& getFloatDataArrays() const;

    FloatDataArrays& getFloatDataArrays();

    void setFloatDataArrays(const FloatDataArrays& fda)
    {
      float_data_arrays_ = fda;
    }

    const StringDataArrays& getStringDataArrays() const;

    StringDataArrays& getStringDataArrays();

    void setStringDataArrays(const StringDataArrays& sda)
    {
      string_data_arrays_ = sda;
    }

    const IntegerDataArrays& getIntegerDataArrays() const;

    IntegerDataArrays& getIntegerDataArrays();

    void setIntegerDataArrays(const IntegerDataArrays& ida)
    {
      integer_data_arrays_ = ida;
    }



    void sortByIntensity(bool reverse = false);

    void sortByPosition();

    bool isSorted() const;



    Size findNearest(CoordinateType rt) const;

    Iterator RTBegin(CoordinateType rt);

    Iterator RTBegin(Iterator begin, CoordinateType rt, Iterator end);

    Iterator RTEnd(CoordinateType rt);

    Iterator RTEnd(Iterator begin, CoordinateType rt, Iterator end);

    ConstIterator RTBegin(CoordinateType rt) const;

    ConstIterator RTBegin(ConstIterator begin, CoordinateType rt, ConstIterator end) const;

    ConstIterator RTEnd(CoordinateType rt) const;

    ConstIterator MZEnd(CoordinateType rt) const;

    ConstIterator RTEnd(ConstIterator begin, CoordinateType rt, ConstIterator end) const;

    Iterator PosBegin(CoordinateType rt);

    Iterator PosBegin(Iterator begin, CoordinateType rt, Iterator end);

    ConstIterator PosBegin(CoordinateType rt) const;

    ConstIterator PosBegin(ConstIterator begin, CoordinateType rt, ConstIterator end) const;

    Iterator PosEnd(CoordinateType rt);

    Iterator PosEnd(Iterator begin, CoordinateType rt, Iterator end);

    ConstIterator PosEnd(CoordinateType rt) const;

    ConstIterator PosEnd(ConstIterator begin, CoordinateType rt, ConstIterator end) const;

    void clear(bool clear_meta_data);


    void mergePeaks(MSChromatogram& other, bool add_meta=false);

protected:

    String name_;

    FloatDataArrays float_data_arrays_;

    StringDataArrays string_data_arrays_;

    IntegerDataArrays integer_data_arrays_;
  };

  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const MSChromatogram& chrom);

} // namespace OpenMS