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.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. 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

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

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

Class Members
vector< SiriusAdapterIdentification >	identifications

OpenMS::SiriusMzTabWriter::SiriusSpectrumMSInfo

class OpenMS::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