TransitionTSVFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#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; 
      String transition_name = ""; 
      double CE = -1; 
      double library_intensity = -1; 
      String group_id = ""; 
      bool decoy = false; 
      String PeptideSequence; 
      std::vector<String> ProteinName; 
      String GeneName; 
      String Annotation; 
      String FullPeptideName; 
      String CompoundName; 
      String SMILES; 
      String SumFormula; 
      String Adducts; 
      String precursor_charge; 
      String peptide_group_label; 
      String label_type; 
      String fragment_charge = "NA"; 
      int fragment_nr = -1; 
      double fragment_mzdelta = -1; 
      double drift_time = -1; 
      int fragment_modification = 0; 
      String fragment_type; 
      std::vector<String> uniprot_id; 
      bool detecting_transition = true; 
      bool identifying_transition = false; 
      bool quantifying_transition = true; 
      std::vector<String> peptidoforms; 

      bool isPeptide() const
      {
        return CompoundName.empty() || CompoundName == "NA";
      }
    };


    void TSVToTargetedExperiment_(std::vector<TSVTransition>& transition_list, OpenMS::TargetedExperiment& exp);

    void TSVToTargetedExperiment_(std::vector<TSVTransition>& transition_list, OpenSwath::LightTargetedExperiment& exp);

    TransitionTSVFile::TSVTransition convertTransition_(const ReactionMonitoringTransition* it, OpenMS::TargetedExperiment& targeted_exp);

    void updateMembers_() override;

private:

    // Members
    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 String& str_inp, double & value, bool & spectrast_legacy);

    bool spectrastAnnotationExtract(const String& str_inp, TSVTransition & mytransition);

    void cleanupTransitions_(TSVTransition& mytransition);


    void resolveMixedSequenceGroups_(std::vector<TSVTransition>& transition_list) const;

    void createTransition_(std::vector<TSVTransition>::iterator& tr_it,
                           OpenMS::ReactionMonitoringTransition& rm_trans);

    void createProtein_(String protein_name, const 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 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);

  };
}