Algorithm class behind the SiriusExport tool: writes a SIRIUS .ms input file from MS data and (optionally) a featureXML. More...

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

Inheritance diagram for SiriusExportAlgorithm:

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Collaboration diagram for SiriusExportAlgorithm:

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Public Member Functions
	SiriusExportAlgorithm ()
	Default constructor; installs the export parameters (see class docs)

bool	isFeatureOnly () const
	`true` if only feature-mapped MS2 spectra should be written (parameter `feature_only`)

UInt	getFilterByNumMassTraces () const
	Minimum number of mass traces a feature must have to be retained (parameter `filter_by_num_masstraces`)

double	getPrecursorMzTolerance () const
	Half-width of the precursor m/z window used during MS2-to-feature mapping (unit per precursorMzToleranceUnitIsPPM)

double	getPrecursorRtTolerance () const
	Half-width of the precursor RT window (seconds) used during MS2-to-feature mapping.

bool	precursorMzToleranceUnitIsPPM () const
	`true` if getPrecursorMzTolerance is interpreted as ppm; otherwise as Th

bool	isNoMasstraceInfoIsotopePattern () const
	`true` to suppress mass-trace-derived isotope-pattern hints in the .ms output (parameter `no_masstrace_info_isotope_pattern`)

int	getIsotopePatternIterations () const
	Number of SIRIUS isotope-pattern iterations to record in the .ms output (parameter `isotope_pattern_iterations`)

void	preprocessing (const std::string &featureinfo, const MSExperiment &spectra, FeatureMapping::FeatureMappingInfo &feature_mapping_info, FeatureMapping::FeatureToMs2Indices &feature_ms2_indices) const
	Build the feature/MS2 mapping consumed by run() from a featureXML.

void	logFeatureSpectraNumber (const std::string &featureinfo, const FeatureMapping::FeatureToMs2Indices &feature_ms2_indices, const MSExperiment &spectra) const
	Emit `OPENMS_LOG_INFO` messages summarising how many features / MS2 spectra will be processed.

void	run (const StringList &mzML_files, const StringList &featureXML_files, const std::string &out_ms, const std::string &out_compoundinfo) const
	Export the SIRIUS .ms input file (and optional compound-info TSV).

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.

virtual	~DefaultParamHandler ()
	Destructor.

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.

void	setParameters (const Param &param)
	Sets the parameters.

const Param &	getParameters () const
	Non-mutable access to the parameters.

const Param &	getDefaults () const
	Non-mutable access to the default parameters.

const std::string &	getName () const
	Non-mutable access to the name.

void	setName (const std::string &name)
	Mutable access to the name.

const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.

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.

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!

std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

std::string	error_name_
	Name that is displayed in error messages during the parameter checking.

bool	check_defaults_
	If this member is set to false no checking if parameters in done;.

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Detailed Description

Algorithm class behind the SiriusExport tool: writes a SIRIUS .ms input file from MS data and (optionally) a featureXML.

Drives the export pipeline that feeds SIRIUS / CSI:FingerID / AssayGeneratorMetabo:

preprocessing() — optional: load a featureXML, filter features by number of mass traces, build a KDTreeFeatureMaps over them, and assign every MS2 spectrum to its closest feature by precursor (RT, m/z).
logFeatureSpectraNumber() — log how many features / additional MS2 spectra are going to be processed.
run() — write the SIRIUS .ms file and the optional compound-info TSV.

Configurable behaviour is exposed through DefaultParamHandler defaults (see the constructor). The accessors below resolve those parameters by name for callers that prefer typed getters over Param lookups.

Constructor & Destructor Documentation

◆ SiriusExportAlgorithm()

SiriusExportAlgorithm ( )

Default constructor; installs the export parameters (see class docs)

Member Function Documentation

◆ getFilterByNumMassTraces()

UInt getFilterByNumMassTraces ( ) const

inline

Minimum number of mass traces a feature must have to be retained (parameter filter_by_num_masstraces)

◆ getIsotopePatternIterations()

int getIsotopePatternIterations ( ) const

inline

Number of SIRIUS isotope-pattern iterations to record in the .ms output (parameter isotope_pattern_iterations)

◆ getPrecursorMzTolerance()

double getPrecursorMzTolerance ( ) const

inline

Half-width of the precursor m/z window used during MS2-to-feature mapping (unit per precursorMzToleranceUnitIsPPM)

◆ getPrecursorRtTolerance()

double getPrecursorRtTolerance ( ) const

inline

Half-width of the precursor RT window (seconds) used during MS2-to-feature mapping.

◆ isFeatureOnly()

bool isFeatureOnly ( ) const

inline

true if only feature-mapped MS2 spectra should be written (parameter feature_only)

◆ isNoMasstraceInfoIsotopePattern()

bool isNoMasstraceInfoIsotopePattern ( ) const

inline

true to suppress mass-trace-derived isotope-pattern hints in the .ms output (parameter no_masstrace_info_isotope_pattern)

◆ logFeatureSpectraNumber()

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

Emit OPENMS_LOG_INFO messages summarising how many features / MS2 spectra will be processed.

Three modes depending on whether a featureXML is in play:

isFeatureOnly() and featureinfo non-empty: logs assigned-feature count only.
featureinfo non-empty (but not feature-only): logs both assigned-feature count and the number of additional unassigned MS2 spectra.
featureinfo empty: logs the raw MS2 spectrum count in spectra.

Parameters

[in]	featureinfo	Path to featureXML (controls which log branch is taken).
[in]	feature_ms2_indices	Output of preprocessing — feature/MS2 mapping.
[in]	spectra	Spectra container used when no featureXML is given.

◆ precursorMzToleranceUnitIsPPM()

bool precursorMzToleranceUnitIsPPM ( ) const

inline

true if getPrecursorMzTolerance is interpreted as ppm; otherwise as Th

◆ preprocessing()

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

Build the feature/MS2 mapping consumed by run() from a featureXML.

If featureinfo is empty the call is a no-op (both output arguments stay untouched) — in that case run() will treat every MS2 spectrum as unassigned.

If featureinfo is given but isFeatureOnly() is false, the mass-trace filter is silently clamped to 1 (with a warning) so that the adduct annotation on multi-trace features is preserved for MS2 spectra. Features with fewer than getFilterByNumMassTraces() mass traces are then dropped, the survivors are wrapped in a KDTreeFeatureMaps, and MS2 spectra are matched to features via FeatureMapping::assignMS2IndexToFeature using the configured precursor tolerances.

Parameters

[in]	featureinfo	Path to featureXML; if empty, the function is a no-op.
[in]	spectra	Spectra container (MS1 + MS2); only MS2 are mapped.
[out]	feature_mapping_info	Receives the loaded feature maps and the kd-tree built from them.
[out]	feature_ms2_indices	Receives the MS2-to-feature assignment / unassigned-MS2 list.

Exceptions

Exception::FileEmpty If featureinfo is non-empty but the file does not exist or is empty.

◆ run()

void run	(	const StringList &	mzML_files,
		const StringList &	featureXML_files,
		const std::string &	out_ms,
		const std::string &	out_compoundinfo
	)		const

Export the SIRIUS .ms input file (and optional compound-info TSV).

Iterates over mzML_files (and, if non-empty, the same-index entry of featureXML_files for feature-level annotation), runs preprocessing internally, and writes one SIRIUS .ms file at out_ms. If out_compoundinfo is non-empty, also writes a per-compound TSV with provenance/metadata.

Parameters

[in]	mzML_files	Input mzML paths to export.
[in]	featureXML_files	Optional per-mzML featureXML paths (parallel to `mzML_files`, or empty).
[in]	out_ms	Destination SIRIUS .ms file (overwritten).
[in]	out_compoundinfo	Destination compound-info TSV (overwritten); skipped if empty.

Exceptions

Exception::UnableToCreateFile If out_ms cannot be opened for writing.

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SiriusExportAlgorithm()

Member Function Documentation

◆ getFilterByNumMassTraces()

◆ getIsotopePatternIterations()

◆ getPrecursorMzTolerance()

◆ getPrecursorRtTolerance()

◆ isFeatureOnly()

◆ isNoMasstraceInfoIsotopePattern()

◆ logFeatureSpectraNumber()

◆ precursorMzToleranceUnitIsPPM()

◆ preprocessing()

◆ run()