SiriusMSConverter.h File Reference

#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureMapping.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/SpectrumLookup.h>
#include <fstream>

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Classes
class	SiriusMSFile
	Writes a SIRIUS .ms file from an MSExperiment, optionally enriched with feature/adduct/formula annotations. More...
class	SiriusMSFile::AccessionInfo
	Source-file accession metadata of the input mzML, captured for the mzTab-M MS_RUN section. More...
class	SiriusMSFile::CompoundInfo
	Per-compound metadata accumulated while writing the .ms file. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::SiriusMSFile::AccessionInfo

class OpenMS::SiriusMSFile::AccessionInfo

Source-file accession metadata of the input mzML, captured for the mzTab-M MS_RUN section.

Collaboration diagram for SiriusMSFile::AccessionInfo:

Class Members
string	native_id_accession	nativeID accession for mztab-m
string	native_id_type	nativeID type for mztab-m
string	sf_accession	sourcefile accessions for mztab-m
string	sf_filename	sourcefile name for mztab-m
string	sf_path	sourcefile path for mztab-m
string	sf_type	sourcefile type for mztab-m

OpenMS::SiriusMSFile::CompoundInfo

class OpenMS::SiriusMSFile::CompoundInfo

Per-compound metadata accumulated while writing the .ms file.

One entry is appended for every compound block emitted by store. The same data is later serialised via saveFeatureCompoundInfoAsTSV and used by downstream tools to map SIRIUS results back to their originating spectra / features and to populate the mzTab-M SmallMolecule / SmallMoleculeFeature sections.

Collaboration diagram for SiriusMSFile::CompoundInfo:

Class Members
int	charge	precursor/feature charge
string	cmp	query_id used compound in .ms file
string	des	description/name of the compound
string	fid	annotated feature_id (if available)
int	file_index	source file index >
double	fmz	annotated mass of a feature (if available)
string	formula	sumformula of the compound
string	ionization	adduct information
vector< string >	m_ids	native ids and identifier for multiple possible identification via AMS ("|" separator)
string	m_ids_id	concatenated list of native ids and identifier for multiple possible identification via AMS ("|" separator) used for mapping of compounds and the annotated spectrum.
vector< string >	native_ids	native ids of the associated spectra
string	native_ids_id	concatenated list of the associated spectra
double	pint_mono	parent/precursor intensity of the compound
double	pmass	parent/precursor mass of the compound
double	rt	retention time of the compound
vector< string >	scan_indices	index of the associated spectra
string	source_file	sourcefile for mztab-m
string	source_format	format of the sourcefile for mztab-m
string	specref_format	spectra ref format for mztab-m
vector< string >	specrefs	spectra reference for mztab-m