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... | |
MassTrace & | operator= (const MassTrace &) |
Assignment operator. More... | |
PeakType & | operator[] (const Size &mt_idx) |
Random access operator. More... | |
const PeakType & | operator[] (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, Size > | getFWHMborders () |
std::pair< Size, Size > | getFWHMborders () const |
std::vector< DoubleReal > | getSmoothedIntensities () |
Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!). More... | |
std::vector< DoubleReal > | getSmoothedIntensities () 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 | |
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. 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< DoubleReal > | smoothed_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 () |
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.
typedef std::vector<PeakType>::const_iterator const_iterator |
typedef std::vector<PeakType>::const_reverse_iterator const_reverse_iterator |
typedef std::vector<PeakType>::reverse_iterator reverse_iterator |
MassTrace | ( | ) |
Default constructor.
MassTrace | ( | const std::list< PeakType > & | , |
const DoubleReal & | scan_time = 1.0 |
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Detailed constructor 1.
MassTrace | ( | const std::vector< PeakType > & | , |
const DoubleReal & | scan_time = 1.0 |
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Detailed constructor 2.
~MassTrace | ( | ) |
Destructor.
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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.
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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).
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Returns the centroid m/z.
Referenced by CmpMassTraceByMZ::operator()().
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Returns the centroid RT.
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ConvexHull2D getConvexhull | ( | ) | const |
Return the mass trace's convex hull.
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DoubleReal getIntensity | ( | bool | ) |
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Gets label of mass trace.
DoubleReal getMaxIntensity | ( | bool | ) |
DoubleReal getMaxIntensity | ( | bool | ) | const |
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Get scan time of mass trace.
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Returns the number of peaks contained in the mass trace.
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Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!).
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Sets label of mass trace.
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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 | ( | ) |
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Centroid m/z.
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Centroid RT.
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intensity-weighted STD
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Trace label.
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Scan time (time difference between two consecutive scans)
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Container for smoothed intensities. Smoothing must be done externally.
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:32 using doxygen 1.8.5 |