Mobilogram.h

Go to the documentation of this file.

// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MobilityPeak1D.h>
#include <OpenMS/KERNEL/PeakContainerSort.h>
#include <OpenMS/METADATA/MetaInfoDescription.h>
#include <OpenMS/KERNEL/RangeManager.h>
#include <OpenMS/METADATA/DataArrays.h>
 
#include <OpenMS/IONMOBILITY/IMTypes.h>
#include <OpenMS/KERNEL/RangeManager.h>
 
#include <algorithm>
#include <numeric>
 
namespace OpenMS
{
  enum class DriftTimeUnit;
  class OPENMS_DLLAPI Mobilogram final : public RangeManagerContainer<RangeMobility, RangeIntensity>
  {
  public:
    struct OPENMS_DLLAPI RTLess {
      bool operator()(const Mobilogram& a, const Mobilogram& b) const;
    };
 
 
 
 
    using PeakType = MobilityPeak1D;
    using CoordinateType = PeakType::CoordinateType;
    using ContainerType = std::vector<PeakType>;
    using RangeManagerContainerType = RangeManagerContainer<RangeMobility, RangeIntensity>;
    using RangeManagerType = RangeManager<RangeMobility, RangeIntensity>;
    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;
 
 
 
    using Iterator = ContainerType::iterator;
    using iterator = Iterator;
    using ConstIterator = ContainerType::const_iterator;
    using const_iterator = ConstIterator;
    using ReverseIterator = ContainerType::reverse_iterator;
    using reverse_iterator = ReverseIterator;
    using ConstReverseIterator = ContainerType::const_reverse_iterator;
    using const_reverse_iterator = ConstReverseIterator;
    /*using typename ContainerType::const_reference;
    using typename ContainerType::difference_type;
    using typename ContainerType::pointer;
    using typename ContainerType::reference;
    using typename ContainerType::size_type;
    using typename ContainerType::value_type;*/
 
    // rule of 6
 
    Mobilogram() = default;
 
    Mobilogram(const Mobilogram& source) = default;
 
    Mobilogram(Mobilogram&&) noexcept = default;
 
    Mobilogram& operator=(const Mobilogram& source) = default;
 
    Mobilogram& operator=(Mobilogram&&) noexcept = default;
 
    ~Mobilogram() = default;
 
 
    bool operator==(const Mobilogram& rhs) const;
 
    bool operator!=(const Mobilogram& rhs) const
    {
      return !(operator==(rhs));
    }
 
 
    MobilityPeak1D& operator[](Size i) noexcept
    {
      return data_[i];  
    }
    const MobilityPeak1D& operator[](Size i) const noexcept
    {
      return data_[i];
    }
 
 
    MobilityPeak1D& front() noexcept
    {
      return data_.front();
    }
    const MobilityPeak1D& front() const noexcept
    {
      return data_.front();
    }
 
    MobilityPeak1D& back() noexcept
    {
      return data_.back();
    }
    const MobilityPeak1D& back() const noexcept
    {
      return data_.back();
    }
 
    Iterator begin() noexcept
    {
      return data_.begin();
    }
    ConstIterator begin() const noexcept
    {
      return data_.begin();
    }
    ConstIterator cbegin() const noexcept
    {
      return data_.cbegin();
    }
 
    Iterator end() noexcept
    {
      return data_.end();
    }
    ConstIterator end() const noexcept
    {
      return data_.end();
    }
    ConstIterator cend() const noexcept
    {
      return data_.cend();
    }
 
    ReverseIterator rbegin() noexcept
    {
      return data_.rbegin();
    }
    ConstReverseIterator crbegin() const
    {
      return data_.crbegin();
    }
    ReverseIterator rend() noexcept
    {
      return data_.rend();
    }
    ConstReverseIterator crend() const
    {
      return data_.crend();
    }
 
    bool empty() const noexcept
    {
      return data_.empty();
    }
    ConstIterator erase(ConstIterator where) noexcept
    {
      return data_.erase(where);
    }
 
    void push_back(MobilityPeak1D mb)
    {
      data_.push_back(mb);
    }
    MobilityPeak1D& emplace_back(MobilityPeak1D mb)
    {
      return data_.emplace_back(mb);
    }
    template<class... Args>
    void emplace_back(Args&&... args)
    {
      data_.emplace_back(args...);
    }
 
    void pop_back()
    {
      data_.pop_back();
    }
 
    Iterator insert(ConstIterator where, ConstIterator first, ConstIterator last)
    {
      return data_.insert(where, first, last);
    }
 
    void resize(size_t new_size)
    {
      return data_.resize(new_size);
    }
    void reserve(size_t new_size)
    {
      return data_.reserve(new_size);
    }
 
    size_t size() const noexcept
    {
      return data_.size();
    }
 
    void swap(Mobilogram& mb) noexcept
    {
      data_.swap(mb.data_);
      std::swap(retention_time_, mb.retention_time_);
      std::swap(drift_time_unit_, mb.drift_time_unit_);
    }
 
    // Docu in base class (RangeManager)
    void updateRanges() override;
 
    double getRT() const noexcept
    {
      return retention_time_;
    }
 
    void setRT(double rt) noexcept
    {
      retention_time_ = rt; 
    }
 
    DriftTimeUnit getDriftTimeUnit() const noexcept
    {
      return drift_time_unit_;
    }
 
    std::string getDriftTimeUnitAsString() const;
 
    void setDriftTimeUnit(DriftTimeUnit dt) noexcept;
 
 
    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;
 
    template<class Predicate>
    bool isSorted(const Predicate& lambda) const
    {
      auto value_2_index_wrapper = [this, &lambda](const PeakType& value1, const PeakType& 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)
    {
      // Validate up front, before running the (possibly data-array-indexing) predicate, so a
      // mis-sized array throws instead of being read out of bounds during the sort.
      checkDataArraySizes_();
      // The sorted indices are a permutation of [0, size): in range and duplicate-free by
      // construction, so the unchecked path is safe and skips the redundant bounds re-scan.
      selectUnchecked(Internal::stableSortedIndices(this->size(), lambda));
    }
 
 
 
    Size findNearest(CoordinateType mb) const;
 
    Int findNearest(CoordinateType mb, CoordinateType tolerance) const;
 
    Int findNearest(CoordinateType mb, CoordinateType tolerance_left, CoordinateType tolerance_right) const;
 
    Int findHighestInWindow(CoordinateType mb, CoordinateType tolerance_left, CoordinateType tolerance_right) const;
 
    Iterator MBBegin(CoordinateType mb);
 
    Iterator MBBegin(Iterator begin, CoordinateType mb, Iterator end);
 
    Iterator MBEnd(CoordinateType mb);
 
    Iterator MBEnd(Iterator begin, CoordinateType mb, Iterator end);
 
    ConstIterator MBBegin(CoordinateType mb) const;
 
    ConstIterator MBBegin(ConstIterator begin, CoordinateType mb, ConstIterator end) const;
 
    ConstIterator MBEnd(CoordinateType mb) const;
 
    ConstIterator MBEnd(ConstIterator begin, CoordinateType mb, ConstIterator end) const;
 
    Iterator PosBegin(CoordinateType mb);
 
    Iterator PosBegin(Iterator begin, CoordinateType mb, Iterator end);
 
    ConstIterator PosBegin(CoordinateType mb) const;
 
    ConstIterator PosBegin(ConstIterator begin, CoordinateType mb, ConstIterator end) const;
 
    Iterator PosEnd(CoordinateType mb);
 
    Iterator PosEnd(Iterator begin, CoordinateType mb, Iterator end);
 
    ConstIterator PosEnd(CoordinateType mb) const;
 
    ConstIterator PosEnd(ConstIterator begin, CoordinateType mb, ConstIterator end) const;
 
 
 
    void clear() noexcept;
 
    Mobilogram& select(const std::vector<Size>& indices);
 
    Mobilogram& selectUnchecked(const std::vector<Size>& indices);
 
    ConstIterator getBasePeak() const;
 
    Iterator getBasePeak();
 
    PeakType::IntensityType calculateTIC() const;
 
  protected:
    void checkDataArraySizes_() const;
 
    std::vector<MobilityPeak1D> data_;
 
    double retention_time_ = -1;
 
    DriftTimeUnit drift_time_unit_ = DriftTimeUnit::NONE;
 
    FloatDataArrays float_data_arrays_;
 
    StringDataArrays string_data_arrays_;
 
    IntegerDataArrays integer_data_arrays_;
  };
 
  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const Mobilogram& mb);
} // namespace OpenMS