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 |