OpenSwathOSWParquetReader.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: Justin Sing $
// $Authors: Justin Sing $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <map>
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI OpenSwathOSWParquetReader
  {
  public:
    struct Row
    {
      int64_t feature_id = 0;
      int64_t run_id = 0;
      int64_t precursor_id = 0;
      double exp_rt = 0.0;
      double ms2_area_intensity = 0.0;
      double ms2_total_area_intensity = 0.0;
      double ms2_apex_intensity = 0.0;
      int precursor_charge = 0;
      bool decoy = false;
      int64_t transition_count = 0;
      std::string group_id;
    };
 
    struct PeakGroupFeatureScoresResult
    {
      // Core per-feature columns (all length N)
      std::vector<int64_t> feature_id;
      std::vector<int64_t> run_id;
      std::vector<int64_t> precursor_id;
      std::vector<double> exp_rt;
      std::vector<int> precursor_charge;
      std::vector<bool> decoy;
      std::vector<int64_t> transition_count;
      std::vector<std::string> group_id;
 
      // Discovered MS2 score columns and their column vectors (each vector length N)
      // ms2_columns[i] corresponds to ms2_values[i]
      std::vector<std::string> ms2_columns;
      std::vector<std::vector<double>> ms2_values;
 
      // Discovered MS1 score columns and their column vectors (only present if requested)
      std::vector<std::string> ms1_columns;
      std::vector<std::vector<double>> ms1_values;
    };
 
    struct TransitionFeaturesResult
    {
      // Core per-transition columns (all length N)
      std::vector<int64_t> feature_id;
      std::vector<int64_t> run_id;
      std::vector<int64_t> precursor_id;
      std::vector<double> exp_rt;
      std::vector<int> precursor_charge;
 
      std::vector<int64_t> transition_id;
      std::vector<int> product_charge;
      std::vector<bool> decoy; // transition-level decoy flag
      std::vector<bool> decoy_valid;
 
      // basic transition-level peak metrics
      std::vector<double> area_intensity;
      std::vector<double> total_area_intensity;
      std::vector<double> apex_intensity;
      std::vector<double> apex_rt;
      std::vector<double> rt_fwhm;
      std::vector<double> masserror_ppm;
      std::vector<double> total_mi;
 
      // Discovered transition-level var_ columns and their column vectors
      std::vector<std::string> transition_var_columns;
      std::vector<std::vector<double>> transition_var_values;
 
      // Group id (run_feature_precursor_transition style)
      std::vector<std::string> group_id;
    };
 
    struct UnscoredResult
    {
      std::vector<int64_t> id_run;
      std::vector<int64_t> id_peptide; 
      std::vector<int64_t> transition_group_id; 
      std::vector<bool> decoy;
      std::vector<int64_t> run_id;
      std::vector<std::string> filename;
      std::vector<double> RT;
      std::vector<double> assay_rt;   // FEATURE.EXP_RT - FEATURE.DELTA_RT
      std::vector<double> delta_rt;   // FEATURE.DELTA_RT
      std::vector<double> assay_RT;   // PRECURSOR.LIBRARY_RT
      std::vector<double> delta_RT;   // FEATURE.NORM_RT - PRECURSOR.LIBRARY_RT
      std::vector<int64_t> id;        // FEATURE.ID
      std::vector<int> Charge;        // PRECURSOR.CHARGE
      std::vector<double> mz;         // PRECURSOR.PRECURSOR_MZ
      std::vector<double> Intensity;  // FEATURE_MS2.AREA_INTENSITY
 
      // aggregated MS1 metrics
      std::vector<double> aggr_prec_Peak_Area;
      std::vector<double> aggr_prec_Peak_Apex;
 
      std::vector<double> leftWidth;
      std::vector<double> rightWidth;
 
      // ion-mobility columns (may be NULL)
      std::vector<double> EXP_IM;
      std::vector<double> IM_leftWidth;
      std::vector<double> IM_rightWidth;
 
      // Discovered score columns (var_ms1_ and var_ms2_) and their values
      std::vector<std::string> ms2_columns;
      std::vector<std::vector<double>> ms2_values;
      std::vector<std::string> ms1_columns;
      std::vector<std::vector<double>> ms1_values;
    };
 
    OpenSwathOSWParquetReader() = default;
 
    OpenSwathOSWParquetReader(const std::string& oswpq_dir);
 
    void load(const std::string& oswpq_dir);
 
    const std::string& oswpqPath() const { return oswpq_dir_; }
 
    const std::vector<Row>& rows() const { return rows_; }
 
    PeakGroupFeatureScoresResult fetchPeakGroupFeatures(const std::string& oswpq_dir, const std::string& level = "ms2", const std::string& main_score = "") const;
 
    TransitionFeaturesResult fetchTransitionFeatures(const std::string& oswpq_dir) const;
 
    UnscoredResult fetchUnscoredData(const std::string& oswpq_dir) const;
 
  private:
    std::vector<Row> rows_;
    // store last-loaded path so Python-side code can call fetch methods without re-supplying the path
    std::string oswpq_dir_;
  };
 
} // namespace OpenMS