30 return lhs->identified_molecule_var.getIdentifiedCompoundRef()->identifier < rhs->identified_molecule_var.getIdentifiedCompoundRef()->identifier;
41 std::map<Size,MzTabParameter>
custom;
106 std::map<Size, MzTabString>
uri;
109 std::map<Size, MzTabSampleMetaData>
sample;
110 std::map<Size, MzTabMMSRunMetaData>
ms_run;
111 std::map<Size, MzTabMAssayMetaData>
assay;
114 std::map<Size, MzTabCVMetaData>
cv;
149 std::vector<MzTabOptionalColumnEntry>
opt_;
169 std::vector<MzTabOptionalColumnEntry>
opt_;
196 std::vector<MzTabOptionalColumnEntry>
opt_;
262 std::vector<MzTabOptionalColumnEntry>& opt,
286 std::set<String>& feature_user_value_keys,
287 std::set<String>& observationmatch_user_value_keys,
288 std::set<String>& compound_user_value_keys);
A container for features.
Definition: FeatureMap.h:80
Definition: MzTabBase.h:361
Definition: MzTabBase.h:79
Definition: MzTabBase.h:41
Definition: MzTabBase.h:101
Data model of MzTab-M files Please see the MzTab-M specification at https://github....
Definition: MzTabM.h:208
MzTabMSmallMoleculeFeatureSectionRows m_small_molecule_feature_data_
Definition: MzTabM.h:275
const std::map< Size, String > & getCommentRows() const
Get comment rows.
MzTabM()=default
Default constructor.
std::vector< Size > empty_rows_
index of empty rows
Definition: MzTabM.h:277
void setMetaData(const MzTabMMetaData &m_md)
Set MzTabMMetaData.
const std::vector< Size > & getEmptyRows() const
Get empty rows.
~MzTabM()=default
Destructor.
static void addMetaInfoToOptionalColumns(const std::set< String > &keys, std::vector< MzTabOptionalColumnEntry > &opt, const String &id, const MetaInfoInterface &meta)
const MzTabMMetaData & getMetaData() const
Extract MzTabMMetaData.
static String getAdductString_(const IdentificationDataInternal::ObservationMatchRef &match_ref)
std::map< Size, String > comment_rows_
comments
Definition: MzTabM.h:278
MzTabMSmallMoleculeEvidenceSectionRows m_small_molecule_evidence_data_
Definition: MzTabM.h:276
void setMSmallMoleculeEvidenceSectionRows(const MzTabMSmallMoleculeEvidenceSectionRows &m_smesd)
Set MzTabMSmallMoleculeEvidenceSectionRows.
std::vector< String > getMSmallMoleculeFeatureOptionalColumnNames() const
Extract opt_ (custom, optional column names)
MzTabMSmallMoleculeSectionRows m_small_molecule_data_
Definition: MzTabM.h:274
static MzTabM exportFeatureMapToMzTabM(const FeatureMap &feature_map)
Export FeatureMap with Identifications to MzTabM.
const MzTabMSmallMoleculeSectionRows & getMSmallMoleculeSectionRows() const
Extract MzTabMSmallMoleculeSectionRows.
const MzTabMSmallMoleculeEvidenceSectionRows & getMSmallMoleculeEvidenceSectionRows() const
Extract MzTabMSmallMoleculeEvidenceSectionRows.
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)
std::vector< String > smf_optional_column_names_
Definition: MzTabM.h:280
std::vector< String > sml_optional_column_names_
Definition: MzTabM.h:279
MzTabMMetaData m_meta_data_
Definition: MzTabM.h:273
void setEmptyRows(const std::vector< Size > &empty)
Set empty rows.
void setMSmallMoleculeFeatureSectionRows(const MzTabMSmallMoleculeFeatureSectionRows &m_smfsd)
Set MzTabMSmallMoleculeFeatureSectionRows.
std::vector< String > getMSmallMoleculeEvidenceOptionalColumnNames() const
Extract opt_ (custom, optional column names)
std::vector< String > sme_optional_column_names_
Definition: MzTabM.h:281
std::vector< String > getMSmallMoleculeOptionalColumnNames() const
Extract opt_ (custom, optional column names)
void setCommentRows(const std::map< Size, String > &com)
Set comment rows.
void setMSmallMoleculeSectionRows(const MzTabMSmallMoleculeSectionRows &m_smsd)
Set MzTabMSmallMoleculeSectionRows.
const MzTabMSmallMoleculeFeatureSectionRows & getMSmallMoleculeFeatureSectionRows() const
Extract MzTabMSmallMoleculeFeatureSectionRows.
Definition: MzTabBase.h:243
Definition: MzTabBase.h:206
Definition: MzTabBase.h:292
Definition: MzTabBase.h:266
Definition: MzTabBase.h:180
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
MzTabSpectraRef spectra_ref
Reference to a spectrum.
Definition: MzTabM.h:191
MzTabDouble calc_mass_to_charge
Precursor ion’s m/z.
Definition: MzTabM.h:190
std::map< Size, MzTabParameter > scan_polarity
The polarity mode of a given run.
Definition: MzTabM.h:58
MzTabString inchi
InChi of the potential compound identifications.
Definition: MzTabM.h:183
MzTabString prefix
The prefix used in the “identifier” column of data tables.
Definition: MzTabM.h:84
MzTabStringList adducts
Adducts.
Definition: MzTabM.h:141
MzTabStringList inchi
InChi of the potential compound identifications.
Definition: MzTabM.h:137
MzTabParameter isotopomer
If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here.
Definition: MzTabM.h:162
MzTabString name
Name of the assay.
Definition: MzTabM.h:40
MzTabString external_uri
A reference to further information about the assay.
Definition: MzTabM.h:42
MzTabParameter format
Parameter specifying the data format of the external MS data file.
Definition: MzTabM.h:55
MzTabParameter derivatized_form
derivatized form.
Definition: MzTabM.h:186
std::map< Size, MzTabDouble > small_molecule_feature_abundance_assay
Feature abundance in every assay.
Definition: MzTabM.h:168
MzTabString sml_identifier
The small molecule’s identifier.
Definition: MzTabM.h:132
MzTabParameter ms_level
The highest MS level used to inform identification.
Definition: MzTabM.h:193
MzTabString smiles
Potential molecular structure as SMILES.
Definition: MzTabM.h:182
MzTabString uri
The URI to the database.
Definition: MzTabM.h:86
std::map< Size, MzTabParameter > fragmentation_method
The type of fragmentation used in a given ms run.
Definition: MzTabM.h:57
std::vector< int > assay_refs
References to the IDs of assays grouped in the study variable.
Definition: MzTabM.h:70
MzTabString reliability
Reliability of the given small molecule identification.
Definition: MzTabM.h:143
std::map< Size, MzTabParameter > custom
Additional parameters or values for a given assay.
Definition: MzTabM.h:41
MzTabInteger sme_id_ref_ambiguity_code
Ambiguity in identifications.
Definition: MzTabM.h:160
MzTabStringList uri
The source entry’s location.
Definition: MzTabM.h:139
MzTabParameter id_format
Parameter specifying the id format used in the external data file.
Definition: MzTabM.h:56
MzTabInteger charge
Precursor ion’s charge.
Definition: MzTabM.h:164
MzTabParameter variation_function
The function used to calculate the study variable quantification variation value.
Definition: MzTabM.h:72
MzTabString adduct
Adduct.
Definition: MzTabM.h:161
MzTabInteger instrument_ref
Link to a specific instrument.
Definition: MzTabM.h:54
MzTabString description
A textual description of the study variable.
Definition: MzTabM.h:73
MzTabStringList chemical_name
Possible chemical/common names or general description.
Definition: MzTabM.h:138
MzTabDouble rt_end
The end time of the feature on the retention time axis.
Definition: MzTabM.h:167
MzTabDouble retention_time
Time point in seconds.
Definition: MzTabM.h:165
MzTabParameter identification_method
Database search, search engine or process that was used to identify this small molecule.
Definition: MzTabM.h:192
MzTabStringList sme_id_refs
Reference to the identification evidence.
Definition: MzTabM.h:159
MzTabParameter average_function
The function used to calculate the study variable quantification value.
Definition: MzTabM.h:71
MzTabString smf_identifier
Within file unique identifier for the small molecule feature.
Definition: MzTabM.h:158
std::map< Size, MzTabDouble > small_molecule_abundance_study_variable
The small molecule’s abundance in all the study variables described in the metadata section.
Definition: MzTabM.h:147
MzTabParameter database
The description of databases used.
Definition: MzTabM.h:83
MzTabDouble rt_start
The start time of the feature on the retention time axis.
Definition: MzTabM.h:166
std::map< Size, MzTabDouble > small_molecule_abundance_variation_study_variable
A measure of the variability of the study variable abundance measurement.
Definition: MzTabM.h:148
MzTabString database_identifier
The putative identification for the small molecule sourced from an external database.
Definition: MzTabM.h:180
std::vector< MzTabMSmallMoleculeFeatureSectionRow > MzTabMSmallMoleculeFeatureSectionRows
Definition: MzTabM.h:200
MzTabStringList database_identifier
Names of the used databases.
Definition: MzTabM.h:134
MzTabStringList smiles
Molecular structure in SMILES format.
Definition: MzTabM.h:136
MzTabString location
Location of the external data file.
Definition: MzTabM.h:53
std::vector< MzTabMSmallMoleculeEvidenceSectionRow > MzTabMSmallMoleculeEvidenceSectionRows
Definition: MzTabM.h:201
MzTabParameter hash_method
Parameter specifying the hash methods.
Definition: MzTabM.h:60
MzTabDoubleList theoretical_neutral_mass
Precursor theoretical neutral mass.
Definition: MzTabM.h:140
MzTabDouble exp_mass_to_charge
Precursor ion’s m/z.
Definition: MzTabM.h:163
MzTabDouble best_id_confidence_value
The best confidence measure.
Definition: MzTabM.h:145
MzTabStringList smf_id_refs
References to all the features on which quantification has been based.
Definition: MzTabM.h:133
std::vector< MzTabOptionalColumnEntry > opt_
Optional columns must start with “opt_”.
Definition: MzTabM.h:149
MzTabString chemical_name
Possible chemical/common names or general description.
Definition: MzTabM.h:184
std::vector< MzTabMSmallMoleculeSectionRow > MzTabMSmallMoleculeSectionRows
Definition: MzTabM.h:199
MzTabString chemical_formula
The putative molecular formula.
Definition: MzTabM.h:181
MzTabString hash
Hash value of the corresponding external MS data file.
Definition: MzTabM.h:59
MzTabString sme_identifier
Within file unique identifier for the small molecule evidence result.
Definition: MzTabM.h:178
MzTabString evidence_input_id
Within file unique identifier for the input data used to support this identification e....
Definition: MzTabM.h:179
std::map< Size, MzTabDouble > small_molecule_abundance_assay
The small molecule’s abundance in every assay described in the metadata section.
Definition: MzTabM.h:146
MzTabParameterList factors
Additional parameters or factors.
Definition: MzTabM.h:74
MzTabInteger sample_ref
An association from a given assay to the sample analysed.
Definition: MzTabM.h:43
std::map< Size, MzTabDouble > id_confidence_measure
Statistical value or score for the identification.
Definition: MzTabM.h:194
MzTabString version
The database version.
Definition: MzTabM.h:85
MzTabInteger rank
Rank of the identification (1 = best)
Definition: MzTabM.h:195
MzTabParameter best_id_confidence_measure
The identification approach with the highest confidence.
Definition: MzTabM.h:144
MzTabInteger ms_run_ref
An association from a given assay to the source MS run.
Definition: MzTabM.h:44
MzTabStringList chemical_formula
Potential chemical formula of the reported compound.
Definition: MzTabM.h:135
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
Data model of MzTabM files. Please see the official MzTabM specification at https://github....
Definition: MzTabM.h:27
bool operator()(const IdentificationDataInternal::ObservationMatchRef &lhs, const IdentificationDataInternal::ObservationMatchRef &rhs) const
Definition: MzTabM.h:28
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:20