SiriusExportAlgorithm Class Reference

#include <OpenMS/ANALYSIS/ID/SiriusExportAlgorithm.h>

Inheritance diagram for SiriusExportAlgorithm:

Collaboration diagram for SiriusExportAlgorithm:

Public Member Functions
	SiriusExportAlgorithm ()
	default constructor More...
bool	isFeatureOnly () const
UInt	getFilterByNumMassTraces () const
double	getPrecursorMzTolerance () const
double	getPrecursorRtTolerance () const
bool	precursorMzToleranceUnitIsPPM () const
bool	isNoMasstraceInfoIsotopePattern () const
int	getIsotopePatternIterations () const
void	preprocessing (const String &featureinfo, const MSExperiment &spectra, FeatureMapping::FeatureMappingInfo &feature_mapping_info, FeatureMapping::FeatureToMs2Indices &feature_ms2_indices) const
	Preprocessing needed for SIRIUS and AssayGeneratorMetabo. More...
void	logFeatureSpectraNumber (const String &featureinfo, const FeatureMapping::FeatureToMs2Indices &feature_ms2_indices, const MSExperiment &spectra) const
	logs number of features and spectra used More...
void	run (const StringList &mzML_files, const StringList &featureXML_files, const String &out_ms, const String &out_compoundinfo) const
	exports SIRIUS .ms file More...
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...
virtual	~DefaultParamHandler ()
	Destructor. More...
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...
void	setParameters (const Param &param)
	Sets the parameters. More...
const Param &	getParameters () const
	Non-mutable access to the parameters. More...
const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...
const String &	getName () const
	Non-mutable access to the name. More...
void	setName (const String &name)
	Mutable access to the name. More...
const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...
Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String	error_name_
	Name that is displayed in error messages during the parameter checking. More...
bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Constructor & Destructor Documentation

SiriusExportAlgorithm()

SiriusExportAlgorithm

(

)

default constructor

Member Function Documentation

getFilterByNumMassTraces()

UInt getFilterByNumMassTraces ( ) const

inline

getIsotopePatternIterations()

int getIsotopePatternIterations ( ) const

inline

getPrecursorMzTolerance()

double getPrecursorMzTolerance ( ) const

inline

getPrecursorRtTolerance()

double getPrecursorRtTolerance ( ) const

inline

isFeatureOnly()

bool isFeatureOnly ( ) const

inline

isNoMasstraceInfoIsotopePattern()

bool isNoMasstraceInfoIsotopePattern ( ) const

inline

logFeatureSpectraNumber()

void logFeatureSpectraNumber	(	const String &	featureinfo,
		const FeatureMapping::FeatureToMs2Indices &	feature_ms2_indices,
		const MSExperiment &	spectra
	)		const

logs number of features and spectra used

Prints the number of features and spectra used (OPENMS_LOG_INFO)

Parameters

featureinfo	Path to featureXML
feature_ms2_indices	FeatureToMs2Indices with feature mapping
spectra	Input of MSExperiment with spectra information

precursorMzToleranceUnitIsPPM()

bool precursorMzToleranceUnitIsPPM ( ) const

inline

preprocessing()

void preprocessing	(	const String &	featureinfo,
		const MSExperiment &	spectra,
		FeatureMapping::FeatureMappingInfo &	feature_mapping_info,
		FeatureMapping::FeatureToMs2Indices &	feature_ms2_indices
	)		const

Preprocessing needed for SIRIUS and AssayGeneratorMetabo.

Filter number of masstraces and perform feature mapping.

Parameters

featureinfo	Path to featureXML
spectra	Input of MSExperiment with spectra information
feature_mapping_info	Emtpy - stores FeatureMaps and KDTreeMaps internally
feature_ms2_indices	Empty FeatureToMs2Indices

run()

void run	(	const StringList &	mzML_files,
		const StringList &	featureXML_files,
		const String &	out_ms,
		const String &	out_compoundinfo
	)		const

exports SIRIUS .ms file

Runs SiriusExport with mzML and featureXML (optional) files as input. Generates a SIRIUS .ms file and compound info table (optional).

Parameters

mzML_files	List with paths to mzML files
featureXML_files	List with paths to featureXML files
out_ms	Output file name for SIRIUS .ms file
out_compoundinfo	Output file name for tsv file with compound info