SiriusMSFile Class Reference

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

Classes
struct	AccessionInfo
struct	CompoundInfo

Static Public Member Functions
static void	store (const PeakMap &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...

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Class Documentation

OpenMS::SiriusMSFile::AccessionInfo

struct OpenMS::SiriusMSFile::AccessionInfo

Class Members
String	native_id_accession
String	native_id_type
String	sf_accession
String	sf_path
String	sf_type

OpenMS::SiriusMSFile::CompoundInfo

struct OpenMS::SiriusMSFile::CompoundInfo

Class Members
int	charge
String	cmp
String	des
String	fid
double	fmz
String	formula
String	ionization
vector< String >	native_ids
double	pmass
double	rt
vector< String >	scan_indices
String	source_file
String	source_format
String	specref_format
vector< String >	specrefs

Member Function Documentation

store()

static void store ( const PeakMap &  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 addded. In this case, SIRIUS assumes default adducts for the respective spectrum.

Returns

writes .ms file

stores CompoundInfo

Parameters

spectra	Peakmap from input mzml.
msfile	Writtes .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.