SiriusMzTabWriter Class Reference

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

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

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

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Class Documentation

OpenMS::SiriusMzTabWriter::SiriusAdapterHit

struct 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
String	precursor_formula
int	rank
double	rank_score
double	sirius_score
double	tree_score

OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification

struct 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

struct OpenMS::SiriusMzTabWriter::SiriusAdapterRun

Collaboration diagram for SiriusMzTabWriter::SiriusAdapterRun:

Class Members
vector< SiriusAdapterIdentification >	identifications

Member Function Documentation

extract_columnname_to_columnindex()

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

static

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.

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