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MassTrace Class Reference

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

#include <OpenMS/KERNEL/MassTrace.h>

Public Member Functions

Constructors and Destructor
 MassTrace ()
 Default constructor. More...
 
 MassTrace (const std::list< PeakType > &, const DoubleReal &scan_time=1.0)
 Detailed constructor 1. More...
 
 MassTrace (const std::vector< PeakType > &, const DoubleReal &scan_time=1.0)
 Detailed constructor 2. More...
 
 ~MassTrace ()
 Destructor. More...
 
 MassTrace (const MassTrace &)
 Copy constructor. More...
 
MassTraceoperator= (const MassTrace &)
 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...
 
DoubleReal getCentroidMZ ()
 Returns the centroid m/z. More...
 
DoubleReal getCentroidMZ () const
 
DoubleReal getCentroidRT ()
 Returns the centroid RT. More...
 
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, SizegetFWHMborders ()
 
std::pair< Size, SizegetFWHMborders () const
 
std::vector< DoubleRealgetSmoothedIntensities ()
 Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!). More...
 
std::vector< DoubleRealgetSmoothedIntensities () const
 
void setSmoothedIntensities (const std::vector< DoubleReal > &db_vec)
 Set smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing). More...
 
DoubleReal getScanTime ()
 Get scan time of mass trace. More...
 
Computational methods
DoubleReal computeSmoothedPeakArea ()
 Sum up mass trace peak intensities for chromatographic peak area estimation. More...
 
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). More...
 
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). More...
 
DoubleReal computeFwhmAreaSmooth ()
 Compute chromatographic peak area within the FWHM range. More...
 
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. 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
 

Update methods for centroid RT and m/z

std::vector< PeakTypetrace_peaks_
 Actual MassTrace container for doing centroid calculation, peak width estimation etc. More...
 
DoubleReal centroid_mz_
 Centroid m/z. More...
 
DoubleReal centroid_sd_
 intensity-weighted STD More...
 
DoubleReal centroid_rt_
 Centroid RT. More...
 
String label_
 Trace label. More...
 
std::vector< DoubleRealsmoothed_intensities_
 Container for smoothed intensities. Smoothing must be done externally. More...
 
DoubleReal fwhm_
 
DoubleReal scan_time_
 Scan time (time difference between two consecutive scans) More...
 
Size fwhm_start_idx_
 
Size fwhm_end_idx_
 
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 ()
 

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>::iterator 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 ( )
inline

Returns the centroid m/z.

Referenced by CmpMassTraceByMZ::operator()().

DoubleReal getCentroidMZ ( ) const
inline
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 ( )
inline

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

std::vector<DoubleReal> getSmoothedIntensities ( ) const
inline
DoubleReal getTraceLength ( )
inline
DoubleReal getTraceLength ( ) const
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
reverse_iterator rend ( )
inline
const_reverse_iterator rend ( ) const
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.


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:32 using doxygen 1.8.5