MRMFeatureAccessOpenMS.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h>
 
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/KERNEL/MRMFeature.h>
#include <OpenMS/KERNEL/MRMTransitionGroup.h>
#include <OpenMS/PROCESSING/NOISEESTIMATION/SignalToNoiseEstimatorMedian.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
 
#include <cstddef>
#include <memory>
#include <string>
#include <utility>
#include <vector>
 
// These classes are minimal implementations of the interfaces defined in ITransition:
//  - IFeature
//  - IMRMFeature
//  - ITransitionGroup
//  - ISignalToNoise
 
namespace OpenMS
{
  class OPENMS_DLLAPI FeatureOpenMS :
    public OpenSwath::IFeature
  {
public:
 
    explicit FeatureOpenMS(const Feature& feature);
 
    ~FeatureOpenMS() override;
 
    void getRT(std::vector<double>& rt) const override;
 
    void getIntensity(std::vector<double>& intens) const override;
 
    float getIntensity() const override;
 
    double getRT() const override;
 
private:
    const Feature* feature_;
  };
 
  class OPENMS_DLLAPI MRMFeatureOpenMS :
    public OpenSwath::IMRMFeature
  {
public:
 
    explicit MRMFeatureOpenMS(MRMFeature& mrmfeature);
 
    MRMFeatureOpenMS(MRMFeature& mrmfeature,
                     const std::vector<std::string>& feature_ids,
                     const std::vector<std::string>& precursor_feature_ids);
 
    MRMFeatureOpenMS(MRMFeature& mrmfeature,
                     const std::vector<std::string>& feature_ids,
                     const std::vector<std::string>& precursor_feature_ids,
                     const std::vector<std::string>& feature_lookup_ids,
                     const std::vector<std::string>& precursor_feature_lookup_ids);
 
    ~MRMFeatureOpenMS() override;
 
    std::shared_ptr<OpenSwath::IFeature> getFeature(std::string nativeID) override;
 
    std::shared_ptr<OpenSwath::IFeature> getPrecursorFeature(std::string nativeID) override;
 
    std::vector<std::string> getNativeIDs() const override;
 
    std::vector<std::string> getPrecursorIDs() const override;
 
    float getIntensity() const override;
 
    double getRT() const override;
 
    double getMetaValue(std::string name) const;
 
    size_t size() const override;
 
    void getFeatureIntensities(const std::vector<std::string>& native_ids, std::vector<std::vector<double>>& intensities) const;
 
    void getPrecursorFeatureIntensities(const std::vector<std::string>& native_ids, std::vector<std::vector<double>>& intensities) const;
 
    float getFeatureIntensity(const std::string& native_id, Size expected_index) const;
 
private:
    struct FeatureLane_;
 
    const MRMFeature& mrmfeature_;
    std::unique_ptr<FeatureLane_> feature_lane_;
    std::unique_ptr<FeatureLane_> precursor_feature_lane_;
  };
 
  template <typename SpectrumT, typename TransitionT>
  class TransitionGroupOpenMS :
    public OpenSwath::ITransitionGroup
  {
public:
 
    TransitionGroupOpenMS(MRMTransitionGroup<SpectrumT, TransitionT>& trgroup) :
      trgroup_(trgroup)
    {
    }
 
    ~TransitionGroupOpenMS() override
    {
    }
 
    std::size_t size() const override
    {
      return trgroup_.size();
    }
 
    std::vector<std::string> getNativeIDs() const override
    {
      std::vector<std::string> result;
      for (std::size_t i = 0; i < this->size(); i++)
      {
        result.push_back(trgroup_.getChromatograms()[i].getNativeID());
      }
      return result;
    }
 
    void getLibraryIntensities(std::vector<double>& intensities) const override
    {
      trgroup_.getLibraryIntensity(intensities);
    }
 
private:
    const MRMTransitionGroup<SpectrumT, TransitionT>& trgroup_;
  };
 
  template <typename ContainerT>
  class SignalToNoiseOpenMS :
    public OpenSwath::ISignalToNoise
  {
public:
 
    SignalToNoiseOpenMS(const ContainerT& chromat,
                        double sn_win_len_, unsigned int sn_bin_count_, bool write_log_messages) :
      chromatogram_(chromat)
    {
      // Only the S/N values are kept, not an estimator: constructing a SignalToNoiseEstimatorMedian builds and
      // checks its whole parameter set, which costs more than the estimate itself, and there is one chromatogram
      // per transition, millions in a DIA run.
      typename SignalToNoiseEstimatorMedian<ContainerT>::Settings settings;
      settings.win_len = sn_win_len_;
      settings.bin_count = static_cast<int>(sn_bin_count_);
      settings.write_log_messages = write_log_messages;
      SignalToNoiseEstimatorMedian<ContainerT>::estimate(chromatogram_, settings, sn_);
    }
 
    double getValueAtRT(double RT) override
    {
      if (chromatogram_.empty()) {return -1;}
 
      // Note that MZBegin does not seem to return the same iterator on
      // different setups, see https://github.com/OpenMS/OpenMS/issues/1163
      auto iter = chromatogram_.PosEnd(RT);
 
      // ensure that iter is valid
      if (iter == chromatogram_.end()) 
      {
        iter--;
      }
 
      auto prev = iter;
      if (prev != chromatogram_.begin()) 
      {
        prev--;
      }
 
      if (std::fabs(prev->getPos() - RT) < std::fabs(iter->getPos() - RT) )
      {
        // prev is closer to the apex
        return sn_[(Size) distance(chromatogram_.begin(),prev)];
      }
      else
      {
        // iter is closer to the apex
        return sn_[(Size) distance(chromatogram_.begin(),iter)];
      }
    }
 
private:
 
    const ContainerT& chromatogram_;
    std::vector<double> sn_;
  };
 
}