MRMFeatureOpenMS Class Reference

An implementation of the OpenSWATH MRM Feature Access interface using OpenMS. More...

#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/MRMFeatureAccessOpenMS.h>

Inheritance diagram for MRMFeatureOpenMS:

Collaboration diagram for MRMFeatureOpenMS:

Public Member Functions
	MRMFeatureOpenMS (MRMFeature &mrmfeature)
	Build access lanes from the native-id maps stored in mrmfeature.
	MRMFeatureOpenMS (MRMFeature &mrmfeature, const std::vector< std::string > &feature_ids, const std::vector< std::string > &precursor_feature_ids)
	Build pointer-based access lanes from explicit fragment and precursor native-id lists.
	MRMFeatureOpenMS (MRMFeature &mrmfeature, const std::vector< std::string > &feature_ids, const std::vector< std::string > &precursor_feature_ids, const std::vector< std::string > &feature_lookup_ids, const std::vector< std::string > &precursor_feature_lookup_ids)
	Build access lanes with externally aligned native-id order.
	~MRMFeatureOpenMS () override
std::shared_ptr< OpenSwath::IFeature >	getFeature (std::string nativeID) override
std::shared_ptr< OpenSwath::IFeature >	getPrecursorFeature (std::string nativeID) override
std::vector< std::string >	getNativeIDs () const override
std::vector< std::string >	getPrecursorIDs () const override
float	getIntensity () const override
double	getRT () const override
double	getMetaValue (std::string name) const
size_t	size () const override
void	getFeatureIntensities (const std::vector< std::string > &native_ids, std::vector< std::vector< double > > &intensities) const
void	getPrecursorFeatureIntensities (const std::vector< std::string > &native_ids, std::vector< std::vector< double > > &intensities) const
float	getFeatureIntensity (const std::string &native_id, Size expected_index) const
	Return the fragment-feature intensity for native_id.
Public Member Functions inherited from IMRMFeature
virtual	~IMRMFeature ()

Private Attributes
const MRMFeature &	mrmfeature_
std::unique_ptr< FeatureLane_ >	feature_lane_
	Fragment-feature access lane. May use aligned ids when the caller provides storage-aligned feature ids.
std::unique_ptr< FeatureLane_ >	precursor_feature_lane_
	Precursor-feature access lane for precursor chromatogram features.

Detailed Description

An implementation of the OpenSWATH MRM Feature Access interface using OpenMS.

Constructor & Destructor Documentation

MRMFeatureOpenMS() [1/3]

MRMFeatureOpenMS ( MRMFeature &  mrmfeature )

explicit

Build access lanes from the native-id maps stored in mrmfeature.

MRMFeatureOpenMS() [2/3]

MRMFeatureOpenMS	(	MRMFeature &	mrmfeature,
		const std::vector< std::string > &	feature_ids,
		const std::vector< std::string > &	precursor_feature_ids
	)

Build pointer-based access lanes from explicit fragment and precursor native-id lists.

MRMFeatureOpenMS() [3/3]

MRMFeatureOpenMS	(	MRMFeature &	mrmfeature,
		const std::vector< std::string > &	feature_ids,
		const std::vector< std::string > &	precursor_feature_ids,
		const std::vector< std::string > &	feature_lookup_ids,
		const std::vector< std::string > &	precursor_feature_lookup_ids
	)

Build access lanes with externally aligned native-id order.

The feature id vectors define the aligned order used for index-hint fast paths. Fragment features are read directly from the underlying MRMFeature storage, so the caller must ensure that feature_ids matches that storage order. The lookup-id vectors are only used to validate and initialize access to the underlying fragment and precursor features.

~MRMFeatureOpenMS()

~MRMFeatureOpenMS ( )

override

Member Function Documentation

getFeature()

std::shared_ptr< OpenSwath::IFeature > getFeature ( std::string  nativeID )

overridevirtual

Implements IMRMFeature.

getFeatureIntensities()

void getFeatureIntensities	(	const std::vector< std::string > &	native_ids,
		std::vector< std::vector< double > > &	intensities
	)		const

getFeatureIntensity()

float getFeatureIntensity	(	const std::string &	native_id,
		Size	expected_index
	)		const

Return the fragment-feature intensity for native_id.

The expected_index parameter is used as an optional fast-path hint. It is only trusted when this object was constructed with externally aligned feature ids. The default MRMFeature native-id order is map-based and must not be assumed to match the underlying feature storage order.

getIntensity()

float getIntensity ( ) const

overridevirtual

Implements IMRMFeature.

getMetaValue()

double getMetaValue ( std::string  name ) const

virtual

Implements IMRMFeature.

getNativeIDs()

std::vector< std::string > getNativeIDs ( ) const

overridevirtual

Implements IMRMFeature.

getPrecursorFeature()

std::shared_ptr< OpenSwath::IFeature > getPrecursorFeature ( std::string  nativeID )

overridevirtual

Implements IMRMFeature.

getPrecursorFeatureIntensities()

void getPrecursorFeatureIntensities	(	const std::vector< std::string > &	native_ids,
		std::vector< std::vector< double > > &	intensities
	)		const

getPrecursorIDs()

std::vector< std::string > getPrecursorIDs ( ) const

overridevirtual

Implements IMRMFeature.

getRT()

double getRT ( ) const

overridevirtual

Implements IMRMFeature.

size()

size_t size ( ) const

overridevirtual

Implements IMRMFeature.

Member Data Documentation

feature_lane_

std::unique_ptr<FeatureLane_> feature_lane_

private

Fragment-feature access lane. May use aligned ids when the caller provides storage-aligned feature ids.

mrmfeature_

const MRMFeature& mrmfeature_

private

precursor_feature_lane_

std::unique_ptr<FeatureLane_> precursor_feature_lane_

private

Precursor-feature access lane for precursor chromatogram features.