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OpenMS
2.5.0
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85 PeakShape(
double height_,
double mz_position_,
double left_width_,
double right_width_,
double area_,
Type type_);
103 double operator()(
double x)
const;
105 double getSymmetricMeasure()
const;
107 double getFWHM()
const;
109 bool iteratorsSet()
const;
Definition: PeakShape.h:70
centroid data or stick data
Definition: SpectrumSettings.h:73
Base class for TOPP applications.
Definition: TOPPBase.h:144
double mz_position
Centroid position.
Definition: PeakShape.h:119
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
bool left_iterator_set_
flag if left endpoint iterator differs from default value
Definition: PeakShape.h:157
This class implements a peak picking algorithm using wavelet techniques.
Definition: PeakPickerCWT.h:78
Type
Peak shape type (asymmetric Lorentzian or asymmetric hyperbolic secans squared).
Definition: PeakShape.h:68
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:58
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
PeakIterator left_endpoint_
Left peak endpoint in the data.
Definition: PeakShape.h:151
void pickExperiment(const PeakMap &input, PeakMap &output)
Picks the peaks in an MSExperiment.
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double left_width
Left width parameter.
Definition: PeakShape.h:121
double signal_to_noise
The signal to noise ratio at the mz_position.
Definition: PeakShape.h:132
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
double area
Area of the peak shape.
Definition: PeakShape.h:125
Size size() const
Definition: MSExperiment.h:127
Definition: PeakShape.h:71
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSSpectrum::const_iterator PeakIterator
Iterator to the raw data vector.
Definition: PeakShape.h:76
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
Type type
peak shape type
Definition: PeakShape.h:135
Internal representation of a peak shape (used by the PeakPickerCWT)
Definition: PeakShape.h:50
double right_width
Right width parameter.
Definition: PeakShape.h:123
Peak picking (conversion from raw to peak data)
Definition: DataProcessing.h:67
double height
Maximum intensity of the peak shape.
Definition: PeakShape.h:117
Exception base class.
Definition: Exception.h:89
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
bool empty() const
Definition: MSExperiment.h:137
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
PeakIterator right_endpoint_
Right peak endpoint in the data.
Definition: PeakShape.h:153
bool operator()(const PeakShape &a, const PeakShape &b)
Definition: PeakShape.h:143
Management and storage of parameters / INI files.
Definition: Param.h:73
void clear(bool clear_meta_data)
Clears all data and meta data.
const char * what() const noexcept override
Returns the error message of the exception.
Comparison of mz_positions.
Definition: PeakShape.h:140
bool right_iterator_set_
flag if left endpoint iterator differs from default value
Definition: PeakShape.h:159
double r_value
Correlation coefficient.
Definition: PeakShape.h:130
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
MSSpectrum exp_
Needed for initialization of endpoint iterators.
Definition: PeakShape.h:155