OpenMS  2.7.0
Public Types | Static Public Member Functions | Public Attributes | Static Public Attributes | Private Member Functions | Private Attributes | List of all members
MassTrace Class Reference

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

#include <OpenMS/KERNEL/MassTrace.h>

Collaboration diagram for MassTrace:
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Public Types

enum  MT_QUANTMETHOD { MT_QUANT_AREA = 0 , MT_QUANT_MEDIAN , MT_QUANT_HEIGHT , SIZE_OF_MT_QUANTMETHOD }
 

Public Member Functions

Constructors and Destructor
 MassTrace ()=default
 Default constructor. More...
 
 MassTrace (const std::list< PeakType > &trace_peaks)
 
 MassTrace (const std::vector< PeakType > &trace_peaks)
 Detailed constructor for vector. More...
 
 ~MassTrace ()=default
 Destructor. More...
 
 MassTrace (const MassTrace &)=default
 Copy constructor. More...
 
MassTraceoperator= (const MassTrace &)=default
 Assignment operator. More...
 
PeakTypeoperator[] (const Size &mt_idx)
 Random access operator. More...
 
const PeakTypeoperator[] (const Size &mt_idx) const
 
Accessor methods
Size getSize () const
 Returns the number of peaks contained in the mass trace. More...
 
String getLabel () const
 Gets label of mass trace. More...
 
void setLabel (const String &label)
 Sets label of mass trace. More...
 
double getCentroidMZ () const
 Returns the centroid m/z. More...
 
double getCentroidRT () const
 Returns the centroid RT. More...
 
double getCentroidSD () const
 
void setCentroidSD (const double &tmp_sd)
 
double getFWHM () const
 
double getTraceLength () const
 Returns the length of the trace (as difference in RT) More...
 
std::pair< Size, SizegetFWHMborders () const
 
const std::vector< double > & getSmoothedIntensities () const
 Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!). More...
 
void setSmoothedIntensities (const std::vector< double > &db_vec)
 Set smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing). More...
 
double getAverageMS1CycleTime () const
 Get average scan time of mass trace. More...
 
Computational methods
double computeSmoothedPeakArea () const
 Sum all non-negative (smoothed!) intensities in the mass trace. More...
 
double computePeakArea () const
 Sum intensities of all peaks in the mass trace. More...
 
Size findMaxByIntPeak (bool use_smoothed_ints=false) const
 Return the index of the mass trace's highest peak within the MassTrace container (based either on raw or smoothed intensities). More...
 
double estimateFWHM (bool use_smoothed_ints=false)
 
void setQuantMethod (MT_QUANTMETHOD method)
 determine if area or median is used for quantification More...
 
MT_QUANTMETHOD getQuantMethod () const
 check if area or median is used for quantification More...
 
double computeFwhmAreaSmooth () const
 Compute chromatographic peak area within the FWHM range. More...
 
double computeFwhmArea () const
 
double getIntensity (bool smoothed) const
 
double getMaxIntensity (bool smoothed) const
 
ConvexHull2D getConvexhull () const
 Return the mass trace's convex hull. More...
 
Update methods for centroid RT and m/z
void updateSmoothedMaxRT ()
 
void updateWeightedMeanRT ()
 Compute & update centroid RT as a intensity-weighted mean of RTs. More...
 
void updateSmoothedWeightedMeanRT ()
 
void updateMedianRT ()
 Compute & update centroid RT as median position of intensities. More...
 
void updateMedianMZ ()
 Compute & update centroid m/z as median of m/z values. More...
 
void updateMeanMZ ()
 Compute & update centroid m/z as mean of m/z values. More...
 
void updateWeightedMeanMZ ()
 Compute & update centroid m/z as weighted mean of m/z values. More...
 
void updateWeightedMZsd ()
 Compute & update m/z standard deviation of mass trace as weighted mean of m/z values. More...
 

Static Public Member Functions

static MT_QUANTMETHOD getQuantMethod (const String &val)
 converts a string to enum value; returns 'SIZE_OF_MT_QUANTMETHOD' upon error More...
 

Public Attributes

double fwhm_mz_avg = 0
 Average FWHM of m/z peaks. More...
 

Static Public Attributes

static const std::string names_of_quantmethod [SIZE_OF_MT_QUANTMETHOD]
 

Private Member Functions

double computeMedianIntensity_ () const
 median of trace intensities More...
 
double linearInterpolationAtY_ (double xA, double xB, double yA, double yB, double y_eval) const
 

Private Attributes

std::vector< PeakTypetrace_peaks_
 Actual MassTrace container for doing centroid calculation, peak width estimation etc. More...
 
double centroid_mz_ = 0.0
 Centroid m/z. More...
 
double centroid_sd_ = 0.0
 intensity-weighted STD More...
 
double centroid_rt_ = 0.0
 Centroid RT. More...
 
String label_
 Trace label. More...
 
std::vector< double > smoothed_intensities_
 Container for smoothed intensities. Smoothing must be done externally. More...
 
double fwhm_ = 0.0
 FWHM of RT peak. More...
 
Size fwhm_start_idx_ = 0
 index into 'trace_peaks_' vector (inclusive) More...
 
Size fwhm_end_idx_ = 0
 index into 'trace_peaks_' vector (inclusive) More...
 
MT_QUANTMETHOD quant_method_ = MT_QUANT_AREA
 use area under mass trace or the median of intensities More...
 

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
 

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 extracted 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

◆ const_iterator

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

◆ const_reverse_iterator

◆ iterator

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

◆ reverse_iterator

Member Enumeration Documentation

◆ MT_QUANTMETHOD

Enumerator
MT_QUANT_AREA 

quantify by area

MT_QUANT_MEDIAN 

quantify by median of intensities

MT_QUANT_HEIGHT 

quantify by peak height

SIZE_OF_MT_QUANTMETHOD 

Constructor & Destructor Documentation

◆ MassTrace() [1/4]

MassTrace ( )
default

Default constructor.

◆ MassTrace() [2/4]

MassTrace ( const std::list< PeakType > &  trace_peaks)

Detailed constructor (useful, since Mass Traces are commonly assembled by prepending and appending – which is faster using lists)

◆ MassTrace() [3/4]

MassTrace ( const std::vector< PeakType > &  trace_peaks)

Detailed constructor for vector.

◆ ~MassTrace()

~MassTrace ( )
default

Destructor.

◆ MassTrace() [4/4]

MassTrace ( const MassTrace )
default

Copy constructor.

Member Function Documentation

◆ begin() [1/2]

iterator begin ( )
inline

◆ begin() [2/2]

const_iterator begin ( ) const
inline

◆ computeFwhmArea()

double computeFwhmArea ( ) const

◆ computeFwhmAreaSmooth()

double computeFwhmAreaSmooth ( ) const

Compute chromatographic peak area within the FWHM range.

◆ computeMedianIntensity_()

double computeMedianIntensity_ ( ) const
private

median of trace intensities

◆ computePeakArea()

double computePeakArea ( ) const

Sum intensities of all peaks in the mass trace.

◆ computeSmoothedPeakArea()

double computeSmoothedPeakArea ( ) const

Sum all non-negative (smoothed!) intensities in the mass trace.

◆ end() [1/2]

iterator end ( )
inline

◆ end() [2/2]

const_iterator end ( ) const
inline

◆ estimateFWHM()

double estimateFWHM ( bool  use_smoothed_ints = false)

Estimate FWHM of chromatographic peak in seconds (based on either raw or smoothed intensities). Uses linear interpolation of the two closest points to the half_max intensity in order to get the RT values at exactly the half_max stores result internally, use getFWHM().

◆ findMaxByIntPeak()

Size findMaxByIntPeak ( bool  use_smoothed_ints = false) const

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

◆ getAverageMS1CycleTime()

double getAverageMS1CycleTime ( ) const
inline

Get average scan time of mass trace.

◆ getCentroidMZ()

double getCentroidMZ ( ) const
inline

Returns the centroid m/z.

Referenced by CmpMassTraceByMZ::operator()().

◆ getCentroidRT()

double getCentroidRT ( ) const
inline

Returns the centroid RT.

◆ getCentroidSD()

double getCentroidSD ( ) const
inline

◆ getConvexhull()

ConvexHull2D getConvexhull ( ) const

Return the mass trace's convex hull.

◆ getFWHM()

double getFWHM ( ) const
inline

◆ getFWHMborders()

std::pair<Size, Size> getFWHMborders ( ) const
inline

◆ getIntensity()

double getIntensity ( bool  smoothed) const

◆ getLabel()

String getLabel ( ) const
inline

Gets label of mass trace.

◆ getMaxIntensity()

double getMaxIntensity ( bool  smoothed) const

◆ getQuantMethod() [1/2]

MT_QUANTMETHOD getQuantMethod ( ) const

check if area or median is used for quantification

◆ getQuantMethod() [2/2]

static MT_QUANTMETHOD getQuantMethod ( const String val)
static

converts a string to enum value; returns 'SIZE_OF_MT_QUANTMETHOD' upon error

◆ getSize()

Size getSize ( ) const
inline

Returns the number of peaks contained in the mass trace.

◆ getSmoothedIntensities()

const std::vector<double>& getSmoothedIntensities ( ) const
inline

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

◆ getTraceLength()

double getTraceLength ( ) const
inline

Returns the length of the trace (as difference in RT)

◆ linearInterpolationAtY_()

double linearInterpolationAtY_ ( double  xA,
double  xB,
double  yA,
double  yB,
double  y_eval 
) const
private

calculate x coordinate of start/end indexes at half_max calculation is based on (yB - yA) / (xB - xA) = (y_eval - yA) / (xC - xA) solve for xC: xC = xA + ((y_eval - yA) * (xB - xA) / (yB - yA))

◆ operator=()

MassTrace& operator= ( const MassTrace )
default

Assignment operator.

◆ operator[]() [1/2]

PeakType& operator[] ( const Size mt_idx)

Random access operator.

◆ operator[]() [2/2]

const PeakType& operator[] ( const Size mt_idx) const

◆ rbegin() [1/2]

reverse_iterator rbegin ( )
inline

◆ rbegin() [2/2]

const_reverse_iterator rbegin ( ) const
inline

◆ rend() [1/2]

reverse_iterator rend ( )
inline

◆ rend() [2/2]

const_reverse_iterator rend ( ) const
inline

◆ setCentroidSD()

void setCentroidSD ( const double &  tmp_sd)
inline

◆ setLabel()

void setLabel ( const String label)
inline

Sets label of mass trace.

◆ setQuantMethod()

void setQuantMethod ( MT_QUANTMETHOD  method)

determine if area or median is used for quantification

◆ setSmoothedIntensities()

void setSmoothedIntensities ( const std::vector< double > &  db_vec)
inline

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

◆ updateMeanMZ()

void updateMeanMZ ( )

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

◆ updateMedianMZ()

void updateMedianMZ ( )

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

◆ updateMedianRT()

void updateMedianRT ( )

Compute & update centroid RT as median position of intensities.

◆ updateSmoothedMaxRT()

void updateSmoothedMaxRT ( )

◆ updateSmoothedWeightedMeanRT()

void updateSmoothedWeightedMeanRT ( )

◆ updateWeightedMeanMZ()

void updateWeightedMeanMZ ( )

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

◆ updateWeightedMeanRT()

void updateWeightedMeanRT ( )

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

◆ updateWeightedMZsd()

void updateWeightedMZsd ( )

Compute & update m/z standard deviation of mass trace as weighted mean of m/z values.

Make sure to call update(Weighted)(Mean|Median)MZ() first!
use getCentroidSD() to get result

Member Data Documentation

◆ centroid_mz_

double centroid_mz_ = 0.0
private

Centroid m/z.

◆ centroid_rt_

double centroid_rt_ = 0.0
private

Centroid RT.

◆ centroid_sd_

double centroid_sd_ = 0.0
private

intensity-weighted STD

◆ fwhm_

double fwhm_ = 0.0
private

FWHM of RT peak.

◆ fwhm_end_idx_

Size fwhm_end_idx_ = 0
private

index into 'trace_peaks_' vector (inclusive)

◆ fwhm_mz_avg

double fwhm_mz_avg = 0

Average FWHM of m/z peaks.

◆ fwhm_start_idx_

Size fwhm_start_idx_ = 0
private

index into 'trace_peaks_' vector (inclusive)

◆ label_

String label_
private

Trace label.

◆ names_of_quantmethod

const std::string names_of_quantmethod[SIZE_OF_MT_QUANTMETHOD]
static

◆ quant_method_

MT_QUANTMETHOD quant_method_ = MT_QUANT_AREA
private

use area under mass trace or the median of intensities

◆ smoothed_intensities_

std::vector<double> smoothed_intensities_
private

Container for smoothed intensities. Smoothing must be done externally.

◆ trace_peaks_

std::vector<PeakType> trace_peaks_
private

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