35 #ifndef OPENMS_KERNEL_MASSTRACE_H
36 #define OPENMS_KERNEL_MASSTRACE_H
90 typedef std::vector<PeakType>::iterator
iterator;
97 return trace_peaks_.begin();
102 return trace_peaks_.end();
107 return trace_peaks_.begin();
112 return trace_peaks_.end();
117 return trace_peaks_.rbegin();
122 return trace_peaks_.rend();
127 return trace_peaks_.rbegin();
132 return trace_peaks_.rend();
141 return trace_peaks_.size();
190 centroid_sd_ = tmp_sd;
207 if (trace_peaks_.size() > 1)
209 length = std::fabs(trace_peaks_.rbegin()->getRT() - trace_peaks_.begin()->getRT());
219 if (trace_peaks_.size() > 1)
221 length = std::fabs(trace_peaks_.rbegin()->getRT() - trace_peaks_.begin()->getRT());
229 return std::make_pair(fwhm_start_idx_, fwhm_end_idx_);
234 return std::make_pair(fwhm_start_idx_, fwhm_end_idx_);
240 return smoothed_intensities_;
245 return smoothed_intensities_;
251 if (trace_peaks_.size() != db_vec.size())
253 throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"Number of smoothed intensities deviates from mass trace size! Aborting...",
String(db_vec.size()));
256 smoothed_intensities_ = db_vec;
275 Size findMaxByIntPeak(
bool)
const;
297 void updateSmoothedMaxRT();
300 void updateWeightedMeanRT();
302 void updateSmoothedWeightedMeanRT();
305 void updateMedianRT();
308 void updateMedianMZ();
314 void updateWeightedMeanMZ();
316 void updateWeightedMZsd();
352 #endif // OPENMS_KERNEL_MASSTRACE_H
DoubleReal getFWHM()
Definition: MassTrace.h:193
DoubleReal centroid_rt_
Centroid RT.
Definition: MassTrace.h:329
iterator end()
Definition: MassTrace.h:100
A more convenient string class.
Definition: String.h:56
DoubleReal centroid_mz_
Centroid m/z.
Definition: MassTrace.h:323
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:55
DoubleReal scan_time_
Scan time (time difference between two consecutive scans)
Definition: MassTrace.h:340
DoubleReal getFWHM() const
Definition: MassTrace.h:198
void setCentroidSD(const DoubleReal &tmp_sd)
Definition: MassTrace.h:188
DoubleReal getTraceLength() const
Definition: MassTrace.h:215
DoubleReal getCentroidSD()
Definition: MassTrace.h:178
Peak2D PeakType
Definition: MassTrace.h:49
DoubleReal fwhm_
Definition: MassTrace.h:337
reverse_iterator rbegin()
Definition: MassTrace.h:115
A 2-dimensional hull representation in [counter]clockwise direction - depending on axis labelling...
Definition: ConvexHull2D.h:75
std::vector< PeakType >::const_iterator const_iterator
Definition: MassTrace.h:91
DoubleReal getCentroidRT() const
Definition: MassTrace.h:173
const_reverse_iterator rbegin() const
Definition: MassTrace.h:125
DoubleReal getCentroidSD() const
Definition: MassTrace.h:183
std::vector< DoubleReal > getSmoothedIntensities()
Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!).
Definition: MassTrace.h:238
std::vector< DoubleReal > getSmoothedIntensities() const
Definition: MassTrace.h:243
DoubleReal getCentroidMZ() const
Definition: MassTrace.h:162
std::vector< PeakType >::iterator iterator
Definition: MassTrace.h:90
DoubleReal centroid_sd_
intensity-weighted STD
Definition: MassTrace.h:326
DoubleReal getScanTime()
Get scan time of mass trace.
Definition: MassTrace.h:260
void setSmoothedIntensities(const std::vector< DoubleReal > &db_vec)
Set smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing). ...
Definition: MassTrace.h:249
std::vector< PeakType >::reverse_iterator reverse_iterator
Definition: MassTrace.h:92
DoubleReal getTraceLength()
Definition: MassTrace.h:203
const_iterator begin() const
Definition: MassTrace.h:105
iterator begin()
Definition: MassTrace.h:95
Size fwhm_end_idx_
Definition: MassTrace.h:343
std::vector< PeakType > trace_peaks_
Actual MassTrace container for doing centroid calculation, peak width estimation etc.
Definition: MassTrace.h:320
std::vector< PeakType >::const_reverse_iterator const_reverse_iterator
Definition: MassTrace.h:93
Invalid value exception.
Definition: Exception.h:336
DoubleReal getCentroidMZ()
Returns the centroid m/z.
Definition: MassTrace.h:157
const_reverse_iterator rend() const
Definition: MassTrace.h:130
reverse_iterator rend()
Definition: MassTrace.h:120
Size fwhm_start_idx_
Definition: MassTrace.h:342
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
void setLabel(const String &label)
Sets label of mass trace.
Definition: MassTrace.h:151
std::pair< Size, Size > getFWHMborders()
Definition: MassTrace.h:227
String getLabel() const
Gets label of mass trace.
Definition: MassTrace.h:145
std::pair< Size, Size > getFWHMborders() const
Definition: MassTrace.h:232
String label_
Trace label.
Definition: MassTrace.h:332
DoubleReal getCentroidRT()
Returns the centroid RT.
Definition: MassTrace.h:168
std::vector< DoubleReal > smoothed_intensities_
Container for smoothed intensities. Smoothing must be done externally.
Definition: MassTrace.h:335
A container type that gathers peaks similar in m/z and moving along retention time.
Definition: MassTrace.h:59
const_iterator end() const
Definition: MassTrace.h:110