TransitionTSVFile.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/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
#include <fstream>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI TransitionTSVFile :
    public ProgressLogger,
    public DefaultParamHandler
  {
 
protected:
    struct TSVTransition
    {
      double precursor = -1; 
      double product = -1; 
      double rt_calibrated = -1; 
      std::string transition_name; 
      double CE = -1; 
      double library_intensity = -1; 
      std::string group_id; 
      bool decoy = false; 
      std::string PeptideSequence; 
      std::vector<std::string> ProteinName; 
      std::string GeneName; 
      std::string Annotation; 
      std::string FullPeptideName; 
      std::string CompoundName; 
      std::string SMILES; 
      std::string SumFormula; 
      std::string Adducts; 
      std::string precursor_charge; 
      std::string peptide_group_label; 
      std::string label_type; 
      std::string fragment_charge = "NA"; 
      int fragment_nr = -1; 
      double fragment_mzdelta = -1; 
      double drift_time = -1; 
      int fragment_modification = 0; 
      std::string fragment_type; 
      std::vector<std::string> uniprot_id; 
      bool detecting_transition = true; 
      bool identifying_transition = false; 
      bool quantifying_transition = true; 
      std::vector<std::string> peptidoforms; 
 
      bool isPeptide() const
      {
        return CompoundName.empty() || CompoundName == "NA";
      }
    };
 
 
    void TSVToTargetedExperiment_(std::vector<TSVTransition>& transition_list, OpenMS::TargetedExperiment& exp);
 
    TransitionTSVFile::TSVTransition convertTransition_(const ReactionMonitoringTransition* it, OpenMS::TargetedExperiment& targeted_exp);
 
    void updateMembers_() override;
 
private:
 
    // Members
    std::string retentionTimeInterpretation_;
    bool override_group_label_check_;
    bool force_invalid_mods_;
 
    // Typedefs
    typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType;
    typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType;
    typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType;
 
    static const char* strarray_[];
 
    static const std::vector<std::string> header_names_;
 
 
    void getTSVHeader_(const std::string& line, char& delimiter, std::map<std::string, int>& header_dict) const;
 
    void readUnstructuredTSVInput_(const char* filename, FileTypes::Type filetype, std::vector<TSVTransition>& transition_list);
 
    void spectrastRTExtract(const std::string& str_inp, double & value, bool & spectrast_legacy);
 
    bool spectrastAnnotationExtract(const std::string& str_inp, TSVTransition & mytransition);
 
    void cleanupTransitions_(TSVTransition& mytransition);
 
    void streamTSVToLightTargetedExperiment_(const char* filename, FileTypes::Type filetype, OpenSwath::LightTargetedExperiment& exp);
 
 
    void resolveMixedSequenceGroups_(std::vector<TSVTransition>& transition_list) const;
 
    void createTransition_(std::vector<TSVTransition>::iterator& tr_it,
                           OpenMS::ReactionMonitoringTransition& rm_trans);
 
    void createProtein_(std::string protein_name, const std::string& uniprot_id,
                        OpenMS::TargetedExperiment::Protein& protein);
 
    void interpretRetentionTime_(std::vector<TargetedExperiment::RetentionTime>& retention_times,
                                 const OpenMS::DataValue& rt_value);
 
    void createPeptide_(std::vector<TSVTransition>::const_iterator tr_it,
                        OpenMS::TargetedExperiment::Peptide& peptide);
 
    void createCompound_(std::vector<TSVTransition>::const_iterator tr_it,
                         OpenMS::TargetedExperiment::Compound& compound);
 
    void addModification_(std::vector<TargetedExperiment::Peptide::Modification>& mods,
                          int location,
                          const ResidueModification& rmod);
 
    void writeTSVOutput_(const char* filename, OpenMS::TargetedExperiment& targeted_exp);
 
public:
 
 
    TransitionTSVFile();
 
    ~TransitionTSVFile() override;
 
    void convertTargetedExperimentToTSV(const char* filename, OpenMS::TargetedExperiment& targeted_exp);
 
    void convertLightTargetedExperimentToTSV(const char* filename, const OpenSwath::LightTargetedExperiment& targeted_exp);
 
    void convertTSVToTargetedExperiment(const char* filename, FileTypes::Type filetype, OpenMS::TargetedExperiment& targeted_exp);
 
    void convertTSVToTargetedExperiment(const char* filename, FileTypes::Type filetype, OpenSwath::LightTargetedExperiment& targeted_exp);
 
    void validateTargetedExperiment(const OpenMS::TargetedExperiment& targeted_exp);
 
  };
}