OSWFile.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: George Rosenberger, Justin Sing $
// $Authors: George Rosenberger, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathExportConfig.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathExportData.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathInferenceConfig.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathInferenceData.h>
#include <OpenMS/DATASTRUCTURES/OSWData.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/FORMAT/SqliteConnector.h>
#include <OpenMS/KERNEL/StandardTypes.h>
 
#include <array>
#include <map>
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI OSWFile
  {
  public:
    
    static constexpr Size ALL_PROTEINS = -1;
 
    OSWFile(const std::string& filename);
    OSWFile(const OSWFile& rhs) = default;
    OSWFile& operator=(const OSWFile& rhs) = default;
 
    void read(OSWData& swath_result);
 
    void readMinimal(OSWData& swath_result);
 
    void readProtein(OSWData& swath_result, const Size index);
 
    enum class OSWLevel
    {
      MS1,
      MS2,
      TRANSITION,
      SIZE_OF_OSWLEVEL
    };
    static const std::array<std::string, (Size)OSWLevel::SIZE_OF_OSWLEVEL> names_of_oswlevel;
 
    struct PercolatorFeature
    {
      PercolatorFeature(double score, double qvalue, double pep)
       : score(score), qvalue(qvalue), posterior_error_prob(pep)
       {}
      PercolatorFeature(const PercolatorFeature& rhs) = default;
      
      double score;
      double qvalue;
      double posterior_error_prob;
    };
 
    static void readToPIN(const std::string& filename, const OSWFile::OSWLevel osw_level, std::ostream& pin_output,
                          const double ipf_max_peakgroup_pep, const double ipf_max_transition_isotope_overlap, const double ipf_min_transition_sn);
 
    static void writeFromPercolator(const std::string& osw_filename, const OSWFile::OSWLevel osw_level, const std::map< std::string, PercolatorFeature >& features);
 
    std::vector<IPFPrecursorRow> readIPFPrecursorData(const PeptidoformInferenceConfig& config) const;
 
    std::vector<IPFTransitionRow> readIPFTransitionData(const PeptidoformInferenceConfig& config) const;
 
    std::vector<IPFAlignmentRow> readIPFAlignmentData(const PeptidoformInferenceConfig& config) const;
 
    std::vector<IPFAlignmentRow> readIPFAlignmentData(double ipf_max_alignment_pep) const;
 
    void writeIPFResults(const std::string& output_filename, const std::vector<IPFResultRow>& results) const;
 
    std::vector<LevelContextInputRow> readLevelContextData(InferenceLevel level, InferenceContext context) const;
 
    void writeLevelContextResults(const std::string& output_filename,
                                  InferenceLevel level,
                                  InferenceContext context,
                                  const std::vector<LevelContextResultRow>& results) const;
 
    std::vector<OpenSwathExportRow> readOpenSwathExportRows(const OpenSwathExportFilterConfig& config) const;
 
    OpenSwathFeatureScoreTable readOpenSwathFeatureScoreTable(const OpenSwathParquetExportConfig& config) const;
 
    OpenSwathTransitionScoreTable readOpenSwathTransitionScoreTable(const OpenSwathParquetExportConfig& config) const;
 
    std::map<Int64, std::string> readRunBasenames() const;
 
    UInt64 getRunID() const;
 
  protected:
    void readTransitions_(OSWData& swath_result);
 
    void getFullProteins_(OSWData& swath_result, Size prot_index = ALL_PROTEINS);
 
    void readMeta_(OSWData& data);
 
  private:
    std::string filename_;       
    SqliteConnector conn_;  
    bool has_SCOREMS2_;     
  };
 
} // namespace OpenMS