MassTrace Class Reference [Kernel]

A container type that gathers peaks similar in m/z and moving along retention time. More...

#include <OpenMS/KERNEL/MassTrace.h>

List of all members.

Public Member Functions
Constructors and Destructor
	MassTrace ()
	Default constructor.
	MassTrace (const std::list< PeakType > &, const DoubleReal &scan_time=1.0)
	Detailed constructor 1.
	MassTrace (const std::vector< PeakType > &, const DoubleReal &scan_time=1.0)
	Detailed constructor 2.
	~MassTrace ()
	Destructor.
	MassTrace (const MassTrace &)
	Copy constructor.
MassTrace &	operator= (const MassTrace &)
	Assignment operator.
PeakType &	operator[] (const Size &mt_idx)
	Random access operator.
const PeakType &	operator[] (const Size &mt_idx) const
Accessor methods
Size	getSize () const
	Returns the number of peaks contained in the mass trace.
String	getLabel () const
	Gets label of mass trace.
void	setLabel (const String &label)
	Sets label of mass trace.
DoubleReal	getCentroidMZ ()
	Returns the centroid m/z.
DoubleReal	getCentroidMZ () const
DoubleReal	getCentroidRT ()
	Returns the centroid RT.
DoubleReal	getCentroidRT () const
DoubleReal	getCentroidSD ()
DoubleReal	getCentroidSD () const
void	setCentroidSD (const DoubleReal &tmp_sd)
DoubleReal	getFWHM ()
DoubleReal	getFWHM () const
DoubleReal	getTraceLength ()
DoubleReal	getTraceLength () const
std::pair< Size, Size >	getFWHMborders ()
std::pair< Size, Size >	getFWHMborders () const
std::vector< DoubleReal >	getSmoothedIntensities ()
	Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!).
std::vector< DoubleReal >	getSmoothedIntensities () const
void	setSmoothedIntensities (const std::vector< DoubleReal > &db_vec)
	Set smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing).
DoubleReal	getScanTime ()
	Get scan time of mass trace.
Computational methods
DoubleReal	computeSmoothedPeakArea ()
	Sum up mass trace peak intensities for chromatographic peak area estimation.
DoubleReal	computePeakArea ()
DoubleReal	computePeakArea () const
Size	findMaxByIntPeak (bool) const
	Return the index of the mass trace's highest peak within the MassTrace container (based either on raw or smoothed intensities).
DoubleReal	estimateFWHM (bool)
	Estimate FWHM of chromatographic peak in seconds (based on either raw or smoothed intensities). As a side-effect, the rough estimation of the number of scans within the FWHM range will be updated (see setFWHMScansNum).
DoubleReal	computeFwhmAreaSmooth ()
	Compute chromatographic peak area within the FWHM range.
DoubleReal	computeFwhmArea ()
DoubleReal	computeFwhmAreaSmoothRobust ()
DoubleReal	computeFwhmAreaRobust ()
DoubleReal	getIntensity (bool)
DoubleReal	getMaxIntensity (bool)
DoubleReal	getMaxIntensity (bool) const
ConvexHull2D	getConvexhull () const
	Return the mass trace's convex hull.
Iterators
Enables mutable/immutable access to the mass trace's peaks.
typedef std::vector< PeakType > ::iterator	iterator
typedef std::vector< PeakType > ::const_iterator	const_iterator
typedef std::vector< PeakType > ::reverse_iterator	reverse_iterator
typedef std::vector< PeakType > ::const_reverse_iterator	const_reverse_iterator
iterator	begin ()
iterator	end ()
const_iterator	begin () const
const_iterator	end () const
reverse_iterator	rbegin ()
reverse_iterator	rend ()
const_reverse_iterator	rbegin () const
const_reverse_iterator	rend () const
Update methods for centroid RT and m/z
std::vector< PeakType >	trace_peaks_
	Actual MassTrace container for doing centroid calculation, peak width estimation etc.
DoubleReal	centroid_mz_
	Centroid m/z.
DoubleReal	centroid_sd_
	intensity-weighted STD
DoubleReal	centroid_rt_
	Centroid RT.
String	label_
	Trace label.
std::vector< DoubleReal >	smoothed_intensities_
	Container for smoothed intensities. Smoothing must be done externally.
DoubleReal	fwhm_
DoubleReal	scan_time_
	Scan time (time difference between two consecutive scans).
Size	fwhm_start_idx_
Size	fwhm_end_idx_
void	updateSmoothedMaxRT ()
void	updateWeightedMeanRT ()
	Compute & update centroid RT as a intensity-weighted mean of RTs.
void	updateSmoothedWeightedMeanRT ()
void	updateMedianRT ()
	Compute & update centroid RT as median position of intensities.
void	updateMedianMZ ()
	Compute & update centroid m/z as median of m/z values.
void	updateMeanMZ ()
	Compute & update centroid m/z as mean of m/z values.
void	updateWeightedMeanMZ ()
	Compute & update centroid m/z as weighted mean of m/z values.
void	updateWeightedMZsd ()

---

Detailed Description

A container type that gathers peaks similar in m/z and moving along retention time.

Depending on the method of extraction a mass trace could virtually represent a complete ion chromatogram (XIC) or merely a part of it (e.g., a chromatographic peak). The kernel class provides methods for computing mass trace characteristics such as its centroid m/z and retention time. Coeluting mass traces can be further assembled to complete isotope patterns of peptides/metabolites.

---

Member Typedef Documentation

typedef std::vector<PeakType>::const_iterator const_iterator

typedef std::vector<PeakType>::const_reverse_iterator const_reverse_iterator

typedef std::vector<PeakType>::iterator iterator

typedef std::vector<PeakType>::reverse_iterator reverse_iterator

---

Constructor & Destructor Documentation

MassTrace

(

)

Default constructor.

MassTrace	(	const std::list< PeakType > &	,
		const DoubleReal &	scan_time = 1.0
	)

Detailed constructor 1.

MassTrace	(	const std::vector< PeakType > &	,
		const DoubleReal &	scan_time = 1.0
	)

Detailed constructor 2.

~MassTrace

(

)

Destructor.

MassTrace

(

const MassTrace &

)

Copy constructor.

---

Member Function Documentation

iterator begin

(

)

[inline]

const_iterator begin

(

)

const [inline]

DoubleReal computeFwhmArea

(

)

DoubleReal computeFwhmAreaRobust

(

)

DoubleReal computeFwhmAreaSmooth

(

)

Compute chromatographic peak area within the FWHM range.

DoubleReal computeFwhmAreaSmoothRobust

(

)

DoubleReal computePeakArea

(

)

DoubleReal computePeakArea

(

)

const

DoubleReal computeSmoothedPeakArea

(

)

Sum up mass trace peak intensities for chromatographic peak area estimation.

iterator end

(

)

[inline]

const_iterator end

(

)

const [inline]

DoubleReal estimateFWHM

(

bool

)

Estimate FWHM of chromatographic peak in seconds (based on either raw or smoothed intensities). As a side-effect, the rough estimation of the number of scans within the FWHM range will be updated (see setFWHMScansNum).

Size findMaxByIntPeak

(

bool

)

const

Return the index of the mass trace's highest peak within the MassTrace container (based either on raw or smoothed intensities).

DoubleReal getCentroidMZ

(

)

const [inline]

DoubleReal getCentroidMZ

(

)

[inline]

Returns the centroid m/z.

Referenced by CmpMassTraceByMZ::operator()().

DoubleReal getCentroidRT

(

)

[inline]

Returns the centroid RT.

DoubleReal getCentroidRT

(

)

const [inline]

DoubleReal getCentroidSD

(

)

[inline]

DoubleReal getCentroidSD

(

)

const [inline]

ConvexHull2D getConvexhull

(

)

const

Return the mass trace's convex hull.

DoubleReal getFWHM

(

)

[inline]

DoubleReal getFWHM

(

)

const [inline]

std::pair<Size, Size> getFWHMborders

(

)

[inline]

std::pair<Size, Size> getFWHMborders

(

)

const [inline]

DoubleReal getIntensity

(

bool

)

String getLabel

(

)

const [inline]

Gets label of mass trace.

DoubleReal getMaxIntensity

(

bool

)

DoubleReal getMaxIntensity

(

bool

)

const

DoubleReal getScanTime

(

)

[inline]

Get scan time of mass trace.

Size getSize

(

)

const [inline]

Returns the number of peaks contained in the mass trace.

std::vector<DoubleReal> getSmoothedIntensities

(

)

const [inline]

std::vector<DoubleReal> getSmoothedIntensities

(

)

[inline]

Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!).

DoubleReal getTraceLength

(

)

const [inline]

DoubleReal getTraceLength

(

)

[inline]

MassTrace& operator=

(

const MassTrace &

)

Assignment operator.

PeakType& operator[]

(

const Size &

mt_idx

)

Random access operator.

const PeakType& operator[]

(

const Size &

mt_idx

)

const

reverse_iterator rbegin

(

)

[inline]

const_reverse_iterator rbegin

(

)

const [inline]

const_reverse_iterator rend

(

)

const [inline]

reverse_iterator rend

(

)

[inline]

void setCentroidSD

(

const DoubleReal &

tmp_sd

)

[inline]

void setLabel

(

const String &

label

)

[inline]

Sets label of mass trace.

void setSmoothedIntensities

(

const std::vector< DoubleReal > &

db_vec

)

[inline]

Set smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing).

void updateMeanMZ

(

)

Compute & update centroid m/z as mean of m/z values.

void updateMedianMZ

(

)

Compute & update centroid m/z as median of m/z values.

void updateMedianRT

(

)

Compute & update centroid RT as median position of intensities.

void updateSmoothedMaxRT

(

)

void updateSmoothedWeightedMeanRT

(

)

void updateWeightedMeanMZ

(

)

Compute & update centroid m/z as weighted mean of m/z values.

void updateWeightedMeanRT

(

)

Compute & update centroid RT as a intensity-weighted mean of RTs.

void updateWeightedMZsd

(

)

---

Member Data Documentation

DoubleReal centroid_mz_ [private]

Centroid m/z.

DoubleReal centroid_rt_ [private]

Centroid RT.

DoubleReal centroid_sd_ [private]

intensity-weighted STD

DoubleReal fwhm_ [private]

Size fwhm_end_idx_ [private]

Size fwhm_start_idx_ [private]

String label_ [private]

Trace label.

DoubleReal scan_time_ [private]

Scan time (time difference between two consecutive scans).

std::vector<DoubleReal> smoothed_intensities_ [private]

Container for smoothed intensities. Smoothing must be done externally.

std::vector<PeakType> trace_peaks_ [private]

Actual MassTrace container for doing centroid calculation, peak width estimation etc.