CsiFingerIdMzTabWriter Class Reference

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

Classes
class	CsiAdapterHit
	Internal structure used in SiriusAdapter that is used for the conversion of the Csi:FingerID output to an mzTab. More...
class	CsiAdapterIdentification
class	CsiAdapterRun

Static Public Member Functions
static void	read (const std::vector< String > &sirius_output_paths, const String &original_input_mzml, const Size &top_n_hits, MzTab &result)
	Conversion of CSI:FingerID output to mzTab. More...

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Class Documentation

OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit

class OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit

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

CsiAdapterHit: inchikey2D (String) inchi (String) rank (int) - Rank of the identification for a compound (spectrum) calculated by CSI:FingerID molecular_formula (String) - sumformula score (int) - Score of the identification for a compound (spectrum) calculated by CSI:FingerID name (String) smiles (String) pubchemids (vector<String>) - PubChemID as reference links (vector<String>) - Links to the database

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

CsiAdapterRun: identifications (vector<CSIAdapterIdentification>)

Collaboration diagram for CsiFingerIdMzTabWriter::CsiAdapterHit:

Class Members
String	adduct
String	dbflags
unsigned int	formula_rank
String	inchi
String	inchikey2D
vector< String >	links
String	molecular_formula
String	name
vector< String >	pubchemids
unsigned int	rank
double	score
String	smiles
String	xlogp

OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification

class OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification

Collaboration diagram for CsiFingerIdMzTabWriter::CsiAdapterIdentification:

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

OpenMS::CsiFingerIdMzTabWriter::CsiAdapterRun

class OpenMS::CsiFingerIdMzTabWriter::CsiAdapterRun

Collaboration diagram for CsiFingerIdMzTabWriter::CsiAdapterRun:

Class Members
vector< CsiAdapterIdentification >	identifications

Member Function Documentation

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 CSI:FingerID output to mzTab.

Output of CSI:FingerID is one directory per spectrum/compound

Parameters

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

Returns

Result written to mzTab