TransitionTSVReader.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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#ifndef OPENMS_ANALYSIS_OPENSWATH_TRANSITIONTSVREADER_H
#define OPENMS_ANALYSIS_OPENSWATH_TRANSITIONTSVREADER_H

#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <fstream>

namespace OpenMS
{

  class OPENMS_DLLAPI TransitionTSVReader :
    public ProgressLogger
  {

private:

    typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType;
    typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType;
    typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType;

    struct TSVTransition
    {
      double precursor;
      double product;
      double rt_calibrated;
      String transition_name;
      double CE;
      double library_intensity;
      String group_id;
      int decoy;
      String PeptideSequence;
      String ProteinName;
      String Annotation;
      String FullPeptideName;
      int precursor_charge;
      String group_label;
      int fragment_charge;
      int fragment_nr;
      String fragment_type;
      String uniprot_id;
    };

    static const char* strarray[];

    static const std::vector<std::string> header_names;

    void readTSVInput_(const char* filename, std::vector<TSVTransition>& transition_list);

    void getTSVHeader(std::string & line, char & delimiter, std::vector<std::string> header, std::map<std::string, int> & header_dict);

    void readUnstructuredTSVInput_(const char* filename, std::vector<TSVTransition>& transition_list);

    void cleanUpTransition(TSVTransition & mytransition);

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

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

    void createProtein_(std::vector<TSVTransition>::iterator& tr_it, OpenMS::TargetedExperiment::Protein& protein);

    void createPeptide_(std::vector<TSVTransition>::iterator& tr_it, OpenMS::TargetedExperiment::Peptide& peptide);

    void add_modification_(std::vector<TargetedExperiment::Peptide::Modification> & mods,
          int location, ResidueModification & rmod, const String & name);


    void writeTSVOutput_(const char* filename, OpenMS::TargetedExperiment& targeted_exp);

public:
    void convertTargetedExperimentToTSV(const char* filename, OpenMS::TargetedExperiment& targeted_exp);

    void convertTSVToTargetedExperiment(const char* filename, OpenMS::TargetedExperiment& targeted_exp);

    void validateTargetedExperiment(OpenMS::TargetedExperiment& targeted_exp);

  };
}

#endif