MzTabM.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/FORMAT/MzTabBase.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/METADATA/ID/IdentificationData.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <set>

namespace OpenMS
{
  struct CompareMzTabMMatchRef
  {
    bool operator() (const IdentificationDataInternal::ObservationMatchRef& lhs, const IdentificationDataInternal::ObservationMatchRef& rhs)  const
    {
      return lhs->identified_molecule_var.getIdentifiedCompoundRef()->identifier < rhs->identified_molecule_var.getIdentifiedCompoundRef()->identifier;
    }
  };

  class OPENMS_DLLAPI MzTabMAssayMetaData
  {
  public:
    MzTabString name; 
    std::map<Size,MzTabParameter> custom; 
    MzTabString external_uri; 
    MzTabInteger sample_ref; 
    MzTabInteger ms_run_ref; 
  };

  class OPENMS_DLLAPI MzTabMMSRunMetaData
  {
  public:
    MzTabString location; 
    MzTabInteger instrument_ref; 
    MzTabParameter format; 
    MzTabParameter id_format; 
    std::map<Size, MzTabParameter> fragmentation_method; 
    std::map<Size, MzTabParameter> scan_polarity; 
    MzTabString hash; 
    MzTabParameter hash_method; 
  };

  class OPENMS_DLLAPI MzTabMStudyVariableMetaData
  {
  public:
    MzTabString name; 
    std::vector<int> assay_refs; 
    MzTabParameter average_function; 
    MzTabParameter variation_function; 
    MzTabString description; 
    MzTabParameterList factors; 
  };

  class OPENMS_DLLAPI MzTabMDatabaseMetaData // mztab-m
  {
  public:
    MzTabParameter database; 
    MzTabString prefix; 
    MzTabString version; 
    MzTabString uri; 
  };

  class OPENMS_DLLAPI MzTabMMetaData
  {
  public:
    MzTabMMetaData();

    MzTabString mz_tab_version; 
    MzTabString mz_tab_id; 
    MzTabString title; 
    MzTabString description; 
    std::map<Size, MzTabParameterList> sample_processing; 
    std::map<Size, MzTabInstrumentMetaData> instrument; 
    std::map<Size, MzTabSoftwareMetaData> software; 
    std::map<Size, MzTabString> publication; 
    std::map<Size, MzTabContactMetaData> contact; 
    std::map<Size, MzTabString> uri; 
    std::map<Size, MzTabString> external_study_uri; 
    MzTabParameter quantification_method; 
    std::map<Size, MzTabSampleMetaData> sample; 
    std::map<Size, MzTabMMSRunMetaData> ms_run; 
    std::map<Size, MzTabMAssayMetaData> assay; 
    std::map<Size, MzTabMStudyVariableMetaData> study_variable; 
    std::map<Size, MzTabParameter> custom; 
    std::map<Size, MzTabCVMetaData> cv; 
    std::map<Size, MzTabMDatabaseMetaData> database; 
    std::map<Size, MzTabParameter> derivatization_agent; 
    MzTabParameter small_molecule_quantification_unit; 
    MzTabParameter small_molecule_feature_quantification_unit; 
    MzTabParameter small_molecule_identification_reliability; 
    std::map<Size, MzTabParameter> id_confidence_measure; 
    std::vector<MzTabString> colunit_small_molecule; 
    std::vector<MzTabString> colunit_small_molecule_feature; 
    std::vector<MzTabString> colunit_small_molecule_evidence; 
  };

  class OPENMS_DLLAPI MzTabMSmallMoleculeSectionRow
  {
  public:
    MzTabString sml_identifier; 
    MzTabStringList smf_id_refs; 
    MzTabStringList database_identifier; 
    MzTabStringList chemical_formula; 
    MzTabStringList smiles; 
    MzTabStringList inchi; 
    MzTabStringList chemical_name; 
    MzTabStringList uri; 
    MzTabDoubleList theoretical_neutral_mass; 
    MzTabStringList adducts; 
    // Reliability information of the used indentificavtion method has to be stored in the ID data structure
    MzTabString reliability; 
    MzTabParameter best_id_confidence_measure; 
    MzTabDouble best_id_confidence_value; 
    std::map<Size, MzTabDouble> small_molecule_abundance_assay; 
    std::map<Size, MzTabDouble> small_molecule_abundance_study_variable; 
    std::map<Size, MzTabDouble> small_molecule_abundance_variation_study_variable; 
    std::vector<MzTabOptionalColumnEntry> opt_; 
  };

  class OPENMS_DLLAPI MzTabMSmallMoleculeFeatureSectionRow
  {
  public:
    MzTabString smf_identifier; 
    MzTabStringList sme_id_refs; 
    MzTabInteger sme_id_ref_ambiguity_code; 
    MzTabString adduct; 
    MzTabParameter isotopomer; 
    MzTabDouble exp_mass_to_charge; 
    MzTabInteger charge; 
    MzTabDouble retention_time; 
    MzTabDouble rt_start; 
    MzTabDouble rt_end; 
    std::map<Size, MzTabDouble> small_molecule_feature_abundance_assay; 
    std::vector<MzTabOptionalColumnEntry> opt_; 
  };

  class OPENMS_DLLAPI MzTabMSmallMoleculeEvidenceSectionRow
  {
  public:
    MzTabString sme_identifier; 
    MzTabString evidence_input_id; 
    MzTabString database_identifier; 
    MzTabString chemical_formula; 
    MzTabString smiles; 
    MzTabString inchi; 
    MzTabString chemical_name; 
    MzTabString uri; 
    MzTabParameter derivatized_form; 
    MzTabString adduct; 
    MzTabDouble exp_mass_to_charge; 
    MzTabInteger charge; 
    MzTabDouble calc_mass_to_charge; 
    MzTabSpectraRef spectra_ref; 
    MzTabParameter identification_method; 
    MzTabParameter ms_level; 
    std::map<Size, MzTabDouble> id_confidence_measure; 
    MzTabInteger rank; 
    std::vector<MzTabOptionalColumnEntry> opt_; 
  };

  typedef std::vector<MzTabMSmallMoleculeSectionRow> MzTabMSmallMoleculeSectionRows;
  typedef std::vector<MzTabMSmallMoleculeFeatureSectionRow> MzTabMSmallMoleculeFeatureSectionRows;
  typedef std::vector<MzTabMSmallMoleculeEvidenceSectionRow> MzTabMSmallMoleculeEvidenceSectionRows;

  class OPENMS_DLLAPI MzTabM : public MzTabBase
  {
  public:
    MzTabM() = default;

    ~MzTabM() = default;

    const MzTabMMetaData& getMetaData() const;

    void setMetaData(const MzTabMMetaData& m_md);

    const MzTabMSmallMoleculeSectionRows& getMSmallMoleculeSectionRows() const;

    void setMSmallMoleculeSectionRows(const MzTabMSmallMoleculeSectionRows& m_smsd);

    const MzTabMSmallMoleculeFeatureSectionRows& getMSmallMoleculeFeatureSectionRows() const;

    void setMSmallMoleculeFeatureSectionRows(const MzTabMSmallMoleculeFeatureSectionRows& m_smfsd);

    const MzTabMSmallMoleculeEvidenceSectionRows& getMSmallMoleculeEvidenceSectionRows() const;

    void setMSmallMoleculeEvidenceSectionRows(const MzTabMSmallMoleculeEvidenceSectionRows& m_smesd);

    void setCommentRows(const std::map<Size, String>& com);

    void setEmptyRows(const std::vector<Size>& empty);

    const std::vector<Size>& getEmptyRows() const;

    const std::map<Size, String>& getCommentRows() const;

    std::vector<String> getMSmallMoleculeOptionalColumnNames() const;

    std::vector<String> getMSmallMoleculeFeatureOptionalColumnNames() const;

    std::vector<String> getMSmallMoleculeEvidenceOptionalColumnNames() const;

    static void addMetaInfoToOptionalColumns(const std::set<String>& keys,
                                             std::vector<MzTabOptionalColumnEntry>& opt,
                                             const String& id, const MetaInfoInterface& meta);

  static MzTabM exportFeatureMapToMzTabM(const FeatureMap& feature_map);

  protected:
    MzTabMMetaData m_meta_data_;
    MzTabMSmallMoleculeSectionRows m_small_molecule_data_;
    MzTabMSmallMoleculeFeatureSectionRows m_small_molecule_feature_data_;
    MzTabMSmallMoleculeEvidenceSectionRows m_small_molecule_evidence_data_;
    std::vector<Size> empty_rows_; 
    std::map<Size, String> comment_rows_; 
    std::vector<String> sml_optional_column_names_;
    std::vector<String> smf_optional_column_names_;
    std::vector<String> sme_optional_column_names_;

    static String getAdductString_(const IdentificationDataInternal::ObservationMatchRef& match_ref);

    static void getFeatureMapMetaValues_(const FeatureMap& feature_map,
                                         std::set<String>& feature_user_value_keys,
                                         std::set<String>& observationmatch_user_value_keys,
                                         std::set<String>& compound_user_value_keys);

  };
} // namespace OpenMS