MultiplexFilteredPeak Class Reference

data structure storing a single peak that passed all filters More...

#include <OpenMS/FEATUREFINDER/MultiplexFilteredPeak.h>

Collaboration diagram for MultiplexFilteredPeak:

Public Member Functions
	MultiplexFilteredPeak (double mz, float rt, size_t mz_idx, size_t rt_idx)
	constructor More...
double	getMZ () const
	returns m/z of the peak More...
float	getRT () const
	returns RT of the peak More...
size_t	getMZidx () const
	returns the index of the peak in the spectrum More...
size_t	getRTidx () const
	returns the index of the corresponding spectrum in the MS experiment More...
void	addSatellite (size_t rt_idx, size_t mz_idx, size_t pattern_idx)
	add a satellite peak More...
void	addSatellite (const MultiplexSatelliteCentroided &satellite, size_t pattern_idx)
void	addSatelliteProfile (float rt, double mz, float intensity, size_t pattern_idx)
	add a satellite data point More...
void	addSatelliteProfile (const MultiplexSatelliteProfile &satellite, size_t pattern_idx)
bool	checkSatellite (size_t rt_idx, size_t mz_idx) const
	check if the peak (rt_idx, mz_idx) is already in the set of satellite peaks More...
const std::multimap< size_t, MultiplexSatelliteCentroided > &	getSatellites () const
	return all satellite peaks More...
const std::multimap< size_t, MultiplexSatelliteProfile > &	getSatellitesProfile () const
	return all satellite data points More...
size_t	size () const
	return number of satellite peaks More...
size_t	sizeProfile () const
	return number of satellite data points More...

Private Attributes
double	mz_
	position of the primary peak More...
float	rt_
size_t	mz_idx_
	indices of the primary peak position in the centroided experiment More...
size_t	rt_idx_
std::multimap< size_t, MultiplexSatelliteCentroided >	satellites_
	set of satellites More...
std::multimap< size_t, MultiplexSatelliteProfile >	satellites_profile_
	set of profile satellites (used on profile data only) More...

Detailed Description

data structure storing a single peak that passed all filters

Each filter result corresponds to a successful search for a particular peak pattern in the centroided data. The actual m/z shifts seen in the filter result might differ from the theoretical shifts listed in the peak pattern.

Each MultiplexFilteredPeak consists of a primary peak and a set of satellite peaks. The primary peak is a peak in the mono-isotopic masstrace of the lightest peptide in the multiplet. The satellite peaks are peaks that form the m/z shift pattern relative to the primary peak within a retention time range rt_band_. They are the evidence on which grounds a peak may pass the filters.

Note that in both centroid and profile mode, centroided data are filtered. (One of the first steps in the profile mode algorithm is the peak picking of the profile data.) Consequently in both modes, centroided peaks make up a final filtered peak.

See also

size(). In profile mode, we additional store the profile data points that make up these peak.

sizeProfile().

MultiplexPeakPattern

Constructor & Destructor Documentation

MultiplexFilteredPeak()

MultiplexFilteredPeak	(	double	mz,
		float	rt,
		size_t	mz_idx,
		size_t	rt_idx
	)

constructor

Member Function Documentation

addSatellite() [1/2]

void addSatellite	(	const MultiplexSatelliteCentroided &	satellite,
		size_t	pattern_idx
	)

addSatellite() [2/2]

void addSatellite	(	size_t	rt_idx,
		size_t	mz_idx,
		size_t	pattern_idx
	)

add a satellite peak

addSatelliteProfile() [1/2]

void addSatelliteProfile	(	const MultiplexSatelliteProfile &	satellite,
		size_t	pattern_idx
	)

addSatelliteProfile() [2/2]

void addSatelliteProfile	(	float	rt,
		double	mz,
		float	intensity,
		size_t	pattern_idx
	)

add a satellite data point

checkSatellite()

bool checkSatellite	(	size_t	rt_idx,
		size_t	mz_idx
	)		const

check if the peak (rt_idx, mz_idx) is already in the set of satellite peaks

getMZ()

double getMZ

(

)

const

returns m/z of the peak

getMZidx()

size_t getMZidx

(

)

const

returns the index of the peak in the spectrum

getRT()

float getRT

(

)

const

returns RT of the peak

getRTidx()

size_t getRTidx

(

)

const

returns the index of the corresponding spectrum in the MS experiment

getSatellites()

const std::multimap<size_t, MultiplexSatelliteCentroided >& getSatellites

(

)

const

return all satellite peaks

See also

also satellites_

getSatellitesProfile()

const std::multimap<size_t, MultiplexSatelliteProfile >& getSatellitesProfile

(

)

const

return all satellite data points

See also

also satellites_profile_

size()

size_t size

(

)

const

return number of satellite peaks

sizeProfile()

size_t sizeProfile

(

)

const

return number of satellite data points

Member Data Documentation

mz_

double mz_

private

position of the primary peak

Position of the primary peak in the m/z-RT plane in [Th, sec]. It is the input for the subsequent clustering step.

mz_idx_

size_t mz_idx_

private

indices of the primary peak position in the centroided experiment

Spectral index and peak index within the spectrum of the primary peak. The indices are used to check the blacklist.

rt_

float rt_

private

rt_idx_

size_t rt_idx_

private

satellites_

std::multimap<size_t, MultiplexSatelliteCentroided > satellites_

private

set of satellites

Mapping from a pattern index i.e. a specific mass trace to all peaks forming the pattern. The primary peak is part of the satellite peak set.

pattern_idx -> (rt_idx, mz_idx)

Typically peaks of the same mass trace show up in neighbouring spectra. The algorithm considers spectra in the RT range rt_band. Consequently, the same pattern_idx key will have multiple associated satellites, and a multimap is required.

Note that we store only indices, not iterators or pointers. We filter 'white' experiments, but all indices refer to the original experiment. White experiments are temporary (for each pattern), but the original exp_picked_ experiment is permanent.

satellites_profile_

std::multimap<size_t, MultiplexSatelliteProfile > satellites_profile_

private

set of profile satellites (used on profile data only)

Mapping from a pattern index i.e. a specific mass trace to all spline-interpolated data points forming the pattern. Basically, when profile data are available as input, we scan over the profile of each satellite peak (see MultiplexSatelliteCentroided above) and decide if it passes the filters or not.

pattern_idx -> (rt, mz, intensity)

Typically peaks of the same mass trace show up in neighbouring spectra. The algorithm considers spectra in the RT range rt_band. Consequently, the same pattern_idx key will have multiple associated satellites, and a multimap is required.