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 2002-2023.
//
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//  * 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.
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//    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.
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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