SiriusMzTabWriter Class Reference

#include <OpenMS/FORMAT/DATAACCESS/SiriusMzTabWriter.h>

Classes
class	SiriusAdapterHit
	Internal structure used in SiriusAdapter that is used for the conversion of the sirius output to an mzTab. More...
class	SiriusAdapterIdentification
class	SiriusAdapterRun
class	SiriusSpectrumMSInfo

Static Public Member Functions
static int	extractScanIndex (const String &path)
	Extract scan_index from filepath. More...
static int	extractScanNumber (const String &path)
	Extract scan_number from filepath. More...
static String	extractFeatureId (const String &path)
	Extract feature_id from filepath. More...
static std::map< std::string, Size >	extract_columnname_to_columnindex (CsvFile &csvfile)
	Extract columnname and index based in SIRIUS entries. More...
static SiriusSpectrumMSInfo	extractSpectrumMSInfo (const String &single_sirius_path)
	Extract mz, rt of the precursor and the nativeID of the corresponding MS2 spectra in the spectrum.ms file. More...
static void	read (const std::vector< String > &sirius_output_paths, const String &original_input_mzml, const Size &top_n_hits, MzTab &result)
	Conversion of sirius output to mzTab. More...

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Class Documentation

OpenMS::SiriusMzTabWriter::SiriusAdapterHit

class OpenMS::SiriusMzTabWriter::SiriusAdapterHit

Internal structure used in SiriusAdapter that is used for the conversion of the sirius output to an mzTab.

SiriusAdapterHit: formula (String) - Sumformula adduct (String) - Assigned adduct precursor_formula (String) - Sumformula of the precursor (can be the same as formula) rank (int) - Rank of the possible sumformula for a compound (spectrum) calculated by Sirius rank_score (double) - Ranking score iso_score (double) - Isotope pattern score tree_score (double) - Fragmentation pattern score sirius_score (double) - Overall score of the possible sumformula for a compound (spectrum) calculated by Sirius explainedpeaks (int) - Number of explained peaks explainedintensity (double) - Relative amount of explained intensity

SiriusAdapterIdentification: scan_index (int) - Index of the spectrum used scan_number (int) - NativeId of the spectrum used feature_id (String) - FeatureId (if spectrum was assigned to a feature) hits (vector<SiriusAdapterHit>)

SiriusAdapterRun: identifications (vector<SiriusAdapterIdentification>)

Store a specific

Parameters

number

of lines from sirius output

Returns

mzTab

Collaboration diagram for SiriusMzTabWriter::SiriusAdapterHit:

Class Members
String	adduct
double	explainedintensity
int	explainedpeaks
String	formula
double	iso_score
double	mass_error_precursor_ppm
double	median_absolute_mass_error_fragment_peaks_ppm
double	median_mass_error_fragment_peaks_ppm
String	precursor_formula
int	rank
double	sirius_score
double	tree_score

OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification

class OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification

Collaboration diagram for SiriusMzTabWriter::SiriusAdapterIdentification:

Class Members
String	feature_id
vector< SiriusAdapterHit >	hits
double	mz
StringList	native_ids
double	rt
int	scan_index
int	scan_number

OpenMS::SiriusMzTabWriter::SiriusAdapterRun

class OpenMS::SiriusMzTabWriter::SiriusAdapterRun

Collaboration diagram for SiriusMzTabWriter::SiriusAdapterRun:

Class Members
vector< SiriusAdapterIdentification >	identifications

OpenMS::SiriusMzTabWriter::SiriusSpectrumMSInfo

class OpenMS::SiriusMzTabWriter::SiriusSpectrumMSInfo

Collaboration diagram for SiriusMzTabWriter::SiriusSpectrumMSInfo:

Class Members
double	ext_mz
StringList	ext_n_id
double	ext_rt

Member Function Documentation

extract_columnname_to_columnindex()

static std::map< std::string, Size > extract_columnname_to_columnindex ( CsvFile &  csvfile )

static

Extract columnname and index based in SIRIUS entries.

extractFeatureId()

static String extractFeatureId ( const String &  path )

static

Extract feature_id from filepath.

extractScanIndex()

static int extractScanIndex ( const String &  path )

static

Extract scan_index from filepath.

extractScanNumber()

static int extractScanNumber ( const String &  path )

static

Extract scan_number from filepath.

extractSpectrumMSInfo()

static SiriusSpectrumMSInfo extractSpectrumMSInfo ( const String &  single_sirius_path )

static

Extract mz, rt of the precursor and the nativeID of the corresponding MS2 spectra in the spectrum.ms file.

read()

static void read ( const std::vector< String > &  sirius_output_paths, const String &  original_input_mzml, const Size &  top_n_hits, MzTab &  result  )

static

Conversion of sirius output to mzTab.

Output of Sirius is one directory per spectrum/compound

Parameters

sirius_output_paths	Path to output directories of Sirius
original_input_mzml	Path to mzml input of SiriusAdapter
top_n_hits	Top n entries for each compound written to the result file

Returns

: Result written to mzTab