Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications. More...

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

Inheritance diagram for IDMapper:

Public Types
enum	Measure { MEASURE_PPM = 0, MEASURE_DA }
Public Member Functions
	IDMapper ()
	Default constructor.
	IDMapper (const IDMapper &cp)
	Copy C'Tor.
IDMapper &	operator= (const IDMapper &rhs)
	Assignment.
template<typename PeakType >
void	annotate (MSExperiment< PeakType > &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids)
	Mapping method for peak maps.
template<typename FeatureType >
void	annotate (FeatureMap< FeatureType > &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool use_centroid_rt=false, bool use_centroid_mz=false)
	Mapping method for feature maps.
void	annotate (ConsensusMap &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool measure_from_subelements=false)
	Mapping method for consensus maps.
Protected Member Functions
void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method.
DoubleReal	getAbsoluteMZTolerance_ (const DoubleReal mz) const
bool	isMatch_ (const DoubleReal rt_distance, const DoubleReal mz_theoretical, const DoubleReal mz_observed) const
	check if distance constraint is fulfilled (using `rt_tolerance_`, `mz_tolerance_` and `measure_`)
void	checkHits_ (const std::vector< PeptideIdentification > &ids) const
	helper function that checks if all peptide hits are annotated with RT and MZ meta values
void	getIDDetails_ (const PeptideIdentification &id, DoubleReal &rt_pep, DoubleList &mz_values, IntList &charges, bool use_avg_mass=false) const
void	increaseBoundingBox_ (DBoundingBox< 2 > &box)
	increase a bounding box by the given RT and m/z tolerances
bool	checkMassType_ (const std::vector< DataProcessing > &processing) const
Protected Attributes
DoubleReal	rt_tolerance_
	Allowed RT deviation.
DoubleReal	mz_tolerance_
	Allowed m/z deviation.
Measure	measure_
	Measure used for m/z.
bool	ignore_charge_
	Ignore charge states during matching?

Detailed Description

Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.

ProteinIdentifications are assigned to the whole map.

The retention time and mass-to-charge ratio of the PeptideIdentification have to be given in the MetaInfoInterface as the values "MZ" and "RT".

m/z-matching on peptide side can be done either with the precursor m/z value of the peptide identification or with the theoretical masses of the peptide hits (see "mz_reference" parameter).

See the documentation of the individual annotate methods for more in-depth information.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
rt_tolerance	float	5	min: 0	RT tolerance (in seconds) for the matching
mz_tolerance	float	20	min: 0	m/z tolerance (in ppm or Da) for the matching
mz_measure	string	ppm	ppm, Da	unit of 'mz_tolerance' (ppm or Da)
mz_reference	string	precursor	precursor, peptide	source of m/z values for peptide identifications
ignore_charge	string	false	true, false	For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Member Enumeration Documentation

enum Measure

Enumerator:

MEASURE_PPM
MEASURE_DA

Constructor & Destructor Documentation

IDMapper ( )

Default constructor.

IDMapper ( const IDMapper & cp )

Copy C'Tor.

Member Function Documentation

void annotate	(	MSExperiment< PeakType > &	map,
		const std::vector< PeptideIdentification > &	ids,
		const std::vector< ProteinIdentification > &	protein_ids
	)			`[inline]`

Mapping method for peak maps.

The identifications stored in a PeptideIdentification instance can be added to the corresponding spectrum.

Parameters:

	map	MSExperiment to receive the identifications
	ids	PeptideIdentification for the ConsensusFeatures
	protein_ids	ProteinIdentification for the ConsensusMap

Exceptions:

Exception::MissingInformation is thrown if the MetaInfoInterface of ids does not contain 'MZ' and 'RT'.

References ExperimentalSettings::getProteinIdentifications(), and LOG_INFO.

Referenced by TOPPViewBase::annotateWithID().

void annotate	(	ConsensusMap &	map,
		const std::vector< PeptideIdentification > &	ids,
		const std::vector< ProteinIdentification > &	protein_ids,
		bool	measure_from_subelements = `false`
	)

Mapping method for consensus maps.

If several consensus features lie inside the allowed deviation, the peptide identifications are mapped to all the consensus features.

Parameters:

	map	ConsensusMap to receive the identifications
	ids	PeptideIdentification for the ConsensusFeatures
	protein_ids	ProteinIdentification for the ConsensusMap
	measure_from_subelements	Do distance estimate from FeatureHandles instead of Centroid

Exceptions:

Exception::MissingInformation is thrown if the MetaInfoInterface of ids does not contain 'MZ' and 'RT'

void annotate	(	FeatureMap< FeatureType > &	map,
		const std::vector< PeptideIdentification > &	ids,
		const std::vector< ProteinIdentification > &	protein_ids,
		bool	use_centroid_rt = `false`,
		bool	use_centroid_mz = `false`
	)			`[inline]`

Mapping method for feature maps.

If all features have at least one convex hull, peptide positions are matched against the bounding boxes of the convex hulls by default. If not, the positions of the feature centroids are used. The respective coordinates of the centroids are also used for matching (in place of the corresponding ranges from the bounding boxes) if use_centroid_rt or use_centroid_mz are true.

In any case, tolerance in RT and m/z dimension is applied according to the global parameters rt_tolerance and mz_tolerance. Tolerance is understood as "plus or minus x", so the matching range is actually increased by twice the tolerance value.

If several features (incl. tolerance) overlap the position of a peptide identification, the identification is annotated to all of them.

Parameters:

	map	FeatureMap to receive the identifications
	ids	PeptideIdentification for the ConsensusFeatures
	protein_ids	ProteinIdentification for the ConsensusMap
	use_centroid_rt	Whether to use the RT value of feature centroids even if convex hulls are present
	use_centroid_mz	Whether to use the m/z value of feature centroids even if convex hulls are present

Exceptions:

Exception::MissingInformation is thrown if the MetaInfoInterface of ids does not contain "MZ" and "RT"

References IntList::contains(), DBoundingBox< D >::encloses(), BaseFeature::getCharge(), Feature::getConvexHulls(), FeatureMap< FeatureT >::getDataProcessing(), BaseFeature::getPeptideIdentifications(), FeatureMap< FeatureT >::getProteinIdentifications(), Peak2D::getRT(), FeatureMap< FeatureT >::getUnassignedPeptideIdentifications(), LOG_INFO, LOG_WARN, DIntervalBase< D >::maxPosition(), DIntervalBase< D >::minPosition(), DIntervalBase< D >::setMaxX(), DIntervalBase< D >::setMaxY(), DIntervalBase< D >::setMinX(), and DIntervalBase< D >::setMinY().

void checkHits_ ( const std::vector< PeptideIdentification > & ids ) const [protected]

helper function that checks if all peptide hits are annotated with RT and MZ meta values

bool checkMassType_ ( const std::vector< DataProcessing > & processing ) const [protected]

try to determine the type of m/z value reported for features, return whether average peptide masses should be used for matching

DoubleReal getAbsoluteMZTolerance_ ( const DoubleReal mz ) const [protected]

compute absolute Da tolerance, for a given m/z, when measure is MEASURE_DA, the value is unchanged, for MEASURE_PPM it is computed according to currently allowed ppm tolerance

void getIDDetails_	(	const PeptideIdentification &	id,
		DoubleReal &	rt_pep,
		DoubleList &	mz_values,
		IntList &	charges,
		bool	use_avg_mass = `false`
	)			const `[protected]`

get RT, m/z and charge value(s) of a PeptideIdentification

multiple m/z values are returned if "mz_reference" is set to "peptide" (one for each PeptideHit)
one m/z value is returned if "mz_reference" is set to "precursor"

void increaseBoundingBox_ ( DBoundingBox< 2 > & box ) [protected]

increase a bounding box by the given RT and m/z tolerances

bool isMatch_	(	const DoubleReal	rt_distance,
		const DoubleReal	mz_theoretical,
		const DoubleReal	mz_observed
	)			const `[protected]`

check if distance constraint is fulfilled (using rt_tolerance_, mz_tolerance_ and measure_)

IDMapper& operator= ( const IDMapper & rhs )

Assignment.

void updateMembers_ ( ) [protected, virtual]

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

bool ignore_charge_ [protected]

Ignore charge states during matching?

Measure measure_ [protected]

Measure used for m/z.

DoubleReal mz_tolerance_ [protected]

Allowed m/z deviation.

DoubleReal rt_tolerance_ [protected]

Allowed RT deviation.

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1

IDMapper Class Reference

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation