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	extract_scan_index (const String &path)
	Extract scan_index 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...

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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 rank (int) - Rank of the possible sumformula for a compound (spectrum) calculated by Sirius score (double) - Overall score of the possible sumformula for a compound (spectrum) calculated by Sirius treescore (double) - Fragmentation pattern score isoscore (double) - Isotope pattern score 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	isoscore
int	rank
double	score
double	treescore

OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification

struct OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification

Collaboration diagram for SiriusMzTabWriter::SiriusAdapterIdentification:

Class Members
String	feature_id
vector< SiriusAdapterHit >	hits
double	mz
String	native_id
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_scan_index()

static int extract_scan_index ( const String &  path )

static

Extract scan_index 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