MSSpectrum.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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//  * 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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// $Maintainer: Timo Sachsenberg$
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/Peak1D.h>
#include <OpenMS/METADATA/SpectrumSettings.h>
#include <OpenMS/KERNEL/RangeManager.h>
#include <OpenMS/METADATA/DataArrays.h>
#include <OpenMS/METADATA/MetaInfoDescription.h>

#include <numeric>

namespace OpenMS
{
  enum class DriftTimeUnit;
  class OPENMS_DLLAPI MSSpectrum final :
    private std::vector<Peak1D>,
    public RangeManagerContainer<RangeMZ, RangeIntensity>,
    public SpectrumSettings
  {
public:

    struct OPENMS_DLLAPI RTLess
    {
      bool operator()(const MSSpectrum& a, const MSSpectrum& b) const;
    };
    struct OPENMS_DLLAPI IMLess {
      bool operator()(const MSSpectrum& a, const MSSpectrum& b) const;
    };

    struct Chunk {
      Size start; 
      Size end; 
      bool is_sorted; 
      Chunk(Size p_start, Size p_end, bool p_sorted) : start(p_start), end(p_end), is_sorted(p_sorted)
      {
      }
    };

    struct Chunks {
      public:
        Chunks(const MSSpectrum& s) : spec_(s) {}
        void add(bool is_sorted)
        {
          chunks_.emplace_back((chunks_.empty() ? 0 : chunks_.back().end), spec_.size(), is_sorted);
        }
        std::vector<Chunk>& getChunks()
        {
          return chunks_;
        }
      private:
        std::vector<Chunk> chunks_;
        const MSSpectrum& spec_;
    };


    typedef OpenMS::Peak1D PeakType;
    typedef typename PeakType::CoordinateType CoordinateType;
    typedef std::vector<PeakType> ContainerType;
    typedef RangeManagerContainer<RangeMZ, RangeIntensity> RangeManagerContainerType;
    typedef RangeManager<RangeMZ, 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::rbegin;
    using ContainerType::end;
    using ContainerType::rend;
    using ContainerType::cbegin;
    using ContainerType::cend;
    using ContainerType::resize;
    using ContainerType::size;
    using ContainerType::push_back;
    using ContainerType::emplace_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;



    MSSpectrum();

    MSSpectrum(const MSSpectrum& source);

    MSSpectrum(MSSpectrum&&) = default;

    ~MSSpectrum() = default;

    MSSpectrum& operator=(const MSSpectrum& source);

    MSSpectrum& operator=(MSSpectrum&&) & = default;

    MSSpectrum& operator=(const SpectrumSettings & source);

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

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

    // Docu in base class (RangeManager)
    void updateRanges() override;

    double getRT() const;

    void setRT(double rt);

    double getDriftTime() const;

    void setDriftTime(double dt);

    DriftTimeUnit getDriftTimeUnit() const;

    String getDriftTimeUnitAsString() const;

    void setDriftTimeUnit(DriftTimeUnit dt);

    UInt getMSLevel() const;

    void setMSLevel(UInt ms_level);

    const String& getName() const;

    void setName(const String& name);


    const FloatDataArrays& getFloatDataArrays() const;

    FloatDataArrays& getFloatDataArrays()
    {
      return float_data_arrays_;
    }

    void setFloatDataArrays(const FloatDataArrays& fda);

    const StringDataArrays& getStringDataArrays() const;

    StringDataArrays& getStringDataArrays();

    void setStringDataArrays(const StringDataArrays& sda);

    const IntegerDataArrays& getIntegerDataArrays() const;

    IntegerDataArrays& getIntegerDataArrays();

    void setIntegerDataArrays(const IntegerDataArrays& ida);



    void sortByIntensity(bool reverse = false);

    void sortByPosition();

    void sortByPositionPresorted(const std::vector<Chunk>& chunks);

    bool isSorted() const;

    template<class Predicate>
    bool isSorted(const Predicate& lambda) const
    {
      auto value_2_index_wrapper = [this, &lambda](const value_type& value1, const value_type& value2) {
        // translate values into indices (this relies on no copies being made!)
        const Size index1 = (&value1) - (&this->front());
        const Size index2 = (&value2) - (&this->front());
        // just make sure the pointers above are actually pointing to a Peak inside our container
        assert(index1 < this->size()); 
        assert(index2 < this->size());
        return lambda(index1, index2);
      }; 
      return std::is_sorted(this->begin(), this->end(), value_2_index_wrapper);
    }

    template<class Predicate> 
    void sort(const Predicate& lambda)
    {
      std::vector<Size> indices(this->size());
      std::iota(indices.begin(), indices.end(), 0);
      std::stable_sort(indices.begin(), indices.end(), lambda);
      select(indices);
    }



    Size findNearest(CoordinateType mz) const;

    Int findNearest(CoordinateType mz, CoordinateType tolerance) const;

    Int findNearest(CoordinateType mz, CoordinateType tolerance_left, CoordinateType tolerance_right) const;

    Int findHighestInWindow(CoordinateType mz, CoordinateType tolerance_left, CoordinateType tolerance_right) const;

    Iterator MZBegin(CoordinateType mz);

    Iterator MZBegin(Iterator begin, CoordinateType mz, Iterator end);

    Iterator MZEnd(CoordinateType mz);

    Iterator MZEnd(Iterator begin, CoordinateType mz, Iterator end);

    ConstIterator MZBegin(CoordinateType mz) const;

    ConstIterator MZBegin(ConstIterator begin, CoordinateType mz, ConstIterator end) const;

    ConstIterator MZEnd(CoordinateType mz) const;

    ConstIterator MZEnd(ConstIterator begin, CoordinateType mz, ConstIterator end) const;

    Iterator PosBegin(CoordinateType mz);

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

    ConstIterator PosBegin(CoordinateType mz) const;

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

    Iterator PosEnd(CoordinateType mz);

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

    ConstIterator PosEnd(CoordinateType mz) const;

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

    bool containsIMData() const;

    std::pair<Size, DriftTimeUnit> getIMData() const;
    


    void clear(bool clear_meta_data);

    /*
      @brief Select a (subset of) spectrum and its data_arrays, only retaining the indices given in @p indices

      @param indices Vector of indices to keep
      @return Reference to this MSSpectrum

    */
    MSSpectrum& select(const std::vector<Size>& indices);


    SpectrumSettings::SpectrumType getType(const bool query_data) const;
    using SpectrumSettings::getType; // expose base class function

    ConstIterator getBasePeak() const;

    Iterator getBasePeak();

    PeakType::IntensityType calculateTIC() const;

protected:
    double retention_time_;

    double drift_time_;

    DriftTimeUnit drift_time_unit_;

    UInt ms_level_;

    String name_;

    FloatDataArrays float_data_arrays_;

    StringDataArrays string_data_arrays_;

    IntegerDataArrays integer_data_arrays_;
  };

  inline std::ostream& operator<<(std::ostream& os, const MSSpectrum& spec)
  {
    os << "-- MSSPECTRUM BEGIN --" << std::endl;

    // spectrum settings
    os << static_cast<const SpectrumSettings&>(spec);

    // peaklist
    for (MSSpectrum::ConstIterator it = spec.begin(); it != spec.end(); ++it)
    {
      os << *it << std::endl;
    }

    os << "-- MSSPECTRUM END --" << std::endl;
    return os;
  }

} // namespace OpenMS