#include <OpenMS/ANALYSIS/ID/SiriusMSConverter.h>

Classes
struct	AccessionInfo

struct	CompoundInfo

Static Public Member Functions
static void	store (const MSExperiment &spectra, const OpenMS::String &msfile, const FeatureMapping::FeatureToMs2Indices &feature_mapping, const bool &feature_only, const int &isotope_pattern_iterations, const bool no_mt_info, std::vector< SiriusMSFile::CompoundInfo > &v_cmpinfo)
	Internal structure used in SiriusAdapter that is used for the conversion of a MzMlFile to an internal format. More...

Static Protected Member Functions
static void	writeMsFile_ (std::ofstream &os, const MSExperiment &spectra, const std::vector< size_t > &ms2_spectra_index, const SiriusMSFile::AccessionInfo &ainfo, const StringList &adducts, const std::vector< String > &v_description, const std::vector< String > &v_sumformula, const std::vector< std::pair< double, double >> &f_isotopes, int &feature_charge, uint64_t &feature_id, const double &feature_rt, const double &feature_mz, bool &writecompound, const bool &no_masstrace_info_isotope_pattern, const int &isotope_pattern_iterations, int &count_skipped_spectra, int &count_assume_mono, int &count_no_ms1, std::vector< SiriusMSFile::CompoundInfo > &v_cmpinfo)
	Internal structure to write the .ms file (called in store function) More...

Class Documentation

◆ OpenMS::SiriusMSFile::AccessionInfo

struct OpenMS::SiriusMSFile::AccessionInfo

Collaboration diagram for SiriusMSFile::AccessionInfo:

[legend]

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_path	sourcefile path for mztab-m
String	sf_type	sourcefile type for mztab-m

◆ OpenMS::SiriusMSFile::CompoundInfo

struct OpenMS::SiriusMSFile::CompoundInfo

Collaboration diagram for SiriusMSFile::CompoundInfo:

[legend]

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)
double	fmz	annotated mass of a feature (if available)
String	formula	sumformula of the compound
String	ionization	adduct information
vector< String >	mids	native ids and identifier for multiple possible identification via AMS
vector< String >	native_ids	native ids 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

Member Function Documentation

◆ store()

static void store	(	const MSExperiment &	spectra,
		const OpenMS::String &	msfile,
		const FeatureMapping::FeatureToMs2Indices &	feature_mapping,
		const bool &	feature_only,
		const int &	isotope_pattern_iterations,
		const bool	no_mt_info,
		std::vector< SiriusMSFile::CompoundInfo > &	v_cmpinfo
	)

static

Internal structure used in SiriusAdapter that is used for the conversion of a MzMlFile to an internal format.

Store .ms file. Comments (see CompoundInfo) are written to SIRIUS .ms file and additionally stores in CompoundInfo struct. If adduct information for a spectrum is missing, no adduct information is added. In this case, SIRIUS assumes default adducts for the respective spectrum.

Returns: writes .ms file; stores CompoundInfo

Parameters

spectra	Peakmap from input mzml.
msfile	Writes .ms file from sirius.
feature_mapping	Adducts and features (index).
feature_only	Only use features.
isotope_pattern_iterations	At which depth to stop isotope_pattern extraction (if possible).
v_cmpinfo	Vector of CompoundInfo.

◆ writeMsFile_()

static void writeMsFile_	(	std::ofstream &	os,
		const MSExperiment &	spectra,
		const std::vector< size_t > &	ms2_spectra_index,
		const SiriusMSFile::AccessionInfo &	ainfo,
		const StringList &	adducts,
		const std::vector< String > &	v_description,
		const std::vector< String > &	v_sumformula,
		const std::vector< std::pair< double, double >> &	f_isotopes,
		int &	feature_charge,
		uint64_t &	feature_id,
		const double &	feature_rt,
		const double &	feature_mz,
		bool &	writecompound,
		const bool &	no_masstrace_info_isotope_pattern,
		const int &	isotope_pattern_iterations,
		int &	count_skipped_spectra,
		int &	count_assume_mono,
		int &	count_no_ms1,
		std::vector< SiriusMSFile::CompoundInfo > &	v_cmpinfo
	)

staticprotected

Internal structure to write the .ms file (called in store function)