TransitionTSVFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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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;
      double product;
      double rt_calibrated;
      String transition_name;
      double CE;
      double library_intensity;
      String group_id;
      bool decoy;
      String PeptideSequence;
      String ProteinName;
      String Annotation;
      String FullPeptideName;
      String CompoundName;
      String SMILES;
      String SumFormula;
      String precursor_charge;
      String peptide_group_label;
      String label_type;
      String fragment_charge;
      int fragment_nr;
      double fragment_mzdelta;
      double drift_time;
      int fragment_modification;
      String fragment_type;
      String uniprot_id;
      bool detecting_transition;
      bool identifying_transition;
      bool quantifying_transition;
      std::vector<String> peptidoforms;

      TSVTransition() :
        precursor(-1),
        product(-1),
        rt_calibrated(-1),
        CE(-1),
        library_intensity(-1),
        decoy(false),
        fragment_charge("NA"),
        fragment_nr(-1),
        fragment_mzdelta(-1),
        drift_time(-1),
        fragment_modification(0),
        detecting_transition(true),
        identifying_transition(false),
        quantifying_transition(true)
      {}

      // By convention, if there is no (metabolic) compound name, it is a peptide 
      bool isPeptide() 
      {
        return CompoundName.empty();
      }
    };

    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:
    String retentionTimeInterpretation_;
    bool override_group_label_check_;
    bool force_invalid_mods_;

    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::vector<std::string> header, std::map<std::string, int>& header_dict);

    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);

    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 interpretRetentionTime_(std::vector<TargetedExperiment::RetentionTime>& retention_times, const OpenMS::DataValue rt_value);

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

    void createCompound_(std::vector<TSVTransition>::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);

  };
}