OpenMS
MzTabMFile.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Oliver Alka $
6 // $Authors: Oliver Alka $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/FORMAT/MzTabM.h>
12 
13 namespace OpenMS
14 {
15  class String;
16  class SVOutStream;
17 
24  class OPENMS_DLLAPI MzTabMFile
25  {
26  public:
29 
32 
34  void store(const String& filename, const MzTabM& mztab_m) const;
35 
36  protected:
37 
44 
52  String generateMzTabMSmallMoleculeHeader_(const MzTabMMetaData& meta, const std::vector<String>& optional_columns, size_t& n_columns) const;
53 
61  String generateMzTabMSmallMoleculeSectionRow_(const MzTabMSmallMoleculeSectionRow& row, const std::vector<String>& optional_columns, size_t& n_columns) const;
62 
70  String generateMzTabMSmallMoleculeFeatureHeader_(const MzTabMMetaData& meta, const std::vector<String>& optional_columns, size_t& n_columns) const;
71 
79  String generateMzTabMSmallMoleculeFeatureSectionRow_(const MzTabMSmallMoleculeFeatureSectionRow& row, const std::vector<String>& optional_columns, size_t& n_columns) const;
80 
88  String generateMzTabMSmallMoleculeEvidenceHeader_(const MzTabMMetaData& meta, const std::vector<String>& optional_columns, size_t& n_columns) const;
89 
97  String generateMzTabMSmallMoleculeEvidenceSectionRow_(const MzTabMSmallMoleculeEvidenceSectionRow& row, const std::vector<String>& optional_columns, size_t& n_columns) const;
98  };
99 
100 } // namespace OpenMS
File adapter for MzTab-M files.
Definition: MzTabMFile.h:25
~MzTabMFile()
Default Destructor.
void generateMzTabMMetaDataSection_(const MzTabMMetaData &map, StringList &sl) const
Generates the MzTabM MetaData Section.
String generateMzTabMSmallMoleculeHeader_(const MzTabMMetaData &meta, const std::vector< String > &optional_columns, size_t &n_columns) const
Generates the MzTabM Small Molecule Header.
void store(const String &filename, const MzTabM &mztab_m) const
Store MzTabM file.
String generateMzTabMSmallMoleculeFeatureHeader_(const MzTabMMetaData &meta, const std::vector< String > &optional_columns, size_t &n_columns) const
Generates the MzTabM Small Molecule Header.
String generateMzTabMSmallMoleculeFeatureSectionRow_(const MzTabMSmallMoleculeFeatureSectionRow &row, const std::vector< String > &optional_columns, size_t &n_columns) const
Generates the MzTabM Small Molecule Feature Section.
String generateMzTabMSmallMoleculeEvidenceSectionRow_(const MzTabMSmallMoleculeEvidenceSectionRow &row, const std::vector< String > &optional_columns, size_t &n_columns) const
Generates the MzTabM Small Molecule Evidence Section.
String generateMzTabMSmallMoleculeSectionRow_(const MzTabMSmallMoleculeSectionRow &row, const std::vector< String > &optional_columns, size_t &n_columns) const
Generates the MzTabM Small Molecule Section.
MzTabMFile()
Default Constructor.
String generateMzTabMSmallMoleculeEvidenceHeader_(const MzTabMMetaData &meta, const std::vector< String > &optional_columns, size_t &n_columns) const
Generates the MzTabM Small Molecule Header.
MztabM Metadata.
Definition: MzTabM.h:93
Data model of MzTab-M files Please see the MzTab-M specification at https://github....
Definition: MzTabM.h:208
A more convenient string class.
Definition: String.h:34
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22
SME Small molecule evidence section (mztab-m)
Definition: MzTabM.h:176
SMF Small molecule feature section (mztab-m)
Definition: MzTabM.h:156
SML Small molecule section (mztab-m)
Definition: MzTabM.h:130