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OpenMS
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57 template <
typename RealT =
double>
92 template <
typename ProbabilityIterator,
typename CoordinateIterator>
93 void update(ProbabilityIterator
const probability_begin,
94 ProbabilityIterator
const probability_end,
95 CoordinateIterator
const coordinate_begin)
98 Base::update(probability_begin, probability_end, coordinate_begin);
106 ProbabilityIterator prob_iter = probability_begin;
107 CoordinateIterator coord_iter = coordinate_begin;
108 for (; prob_iter != probability_end; ++prob_iter, ++coord_iter)
111 RealType diff_squared = diff * diff;
115 if (*coord_iter <
mean_)
128 RealType frac = (diff / stdev + 1.) / 2.;
129 RealType prob_frac = frac * *prob_iter;
132 prob_frac = *prob_iter * (1. - frac);
Base class for TOPP applications.
Definition: TOPPBase.h:150
void addLine(const StringType &line)
Definition: TextFile.h:112
static constexpr const float DEFAULT_BIN_WIDTH_HIRES
Definition: BinnedSpectrum.h:99
Merges blocks of MS or MS2 spectra.
Definition: SpectraMerger.h:63
This is a binned representation of a PeakSpectrum.
Definition: BinnedSpectrum.h:75
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
RealType variance1() const
"variance to the left hand side"
Definition: AsymmetricStatistics.h:80
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
Iterator begin()
Definition: MSExperiment.h:157
A basic LC-MS feature.
Definition: BaseFeature.h:55
Precondition failed exception.
Definition: Exception.h:166
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
RealType sum_
Definition: BasicStatistics.h:258
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
RealType variance2() const
"variance to the right hand side"
Definition: AsymmetricStatistics.h:86
RealType mean_
Definition: BasicStatistics.h:256
String prefix(SizeType length) const
returns the prefix of length length
RealType variance_
Definition: BasicStatistics.h:257
static std::pair< double, double > getTolWindow(double val, double tol, bool ppm)
Return tolerance window around val given tolerance tol.
Definition: MathFunctions.h:296
RealType variance1_
Definition: AsymmetricStatistics.h:144
const BaseFeature * feature(Size i) const
Return pointer to feature i.
profile data
Definition: SpectrumSettings.h:74
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
void clear()
Set sum, mean, and variance to zero.
Definition: BasicStatistics.h:103
Size size() const
Definition: MSExperiment.h:127
ConstIterator getPrecursorSpectrum(ConstIterator iterator) const
Returns the precursor spectrum of the scan pointed to by iterator.
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:111
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
void addMaps(const std::vector< MapType > &maps)
Add maps and balance kd-tree.
Definition: KDTreeFeatureMaps.h:81
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:450
void update(ProbabilityIterator probability_begin, ProbabilityIterator const probability_end)
This does the actual calculation.
Definition: BasicStatistics.h:113
double mz(Size i) const
m/z
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...
SpectrumType
Spectrum peak type.
Definition: SpectrumSettings.h:70
Calculates some basic statistical parameters of a distribution: sum, mean, variance,...
Definition: BasicStatistics.h:67
Internal class for asymmetric distributions.
Definition: AsymmetricStatistics.h:58
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:113
Iterator MZBegin(CoordinateType mz)
Binary search for peak range begin.
void setParameters(const Param ¶m)
Sets the parameters.
void mergeSpectraPrecursors(MapType &exp)
merges spectra with similar precursors (must have MS2 level)
Definition: SpectraMerger.h:209
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
BasicStatistics< RealT > Base
The real type and basic statistics specified as template argument.
Definition: AsymmetricStatistics.h:62
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
A container for features.
Definition: FeatureMap.h:93
An LC-MS feature.
Definition: Feature.h:70
Iterator end()
Definition: MSExperiment.h:167
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
AsymmetricStatistics()
Default constructor.
Definition: AsymmetricStatistics.h:73
void update(ProbabilityIterator const probability_begin, ProbabilityIterator const probability_end, CoordinateIterator const coordinate_begin)
You can call this as often as you like, using different input vectors.
Definition: AsymmetricStatistics.h:93
void store(const String &filename)
Writes the data to a file.
void queryRegion(double rt_low, double rt_high, double mz_low, double mz_high, std::vector< Size > &result_indices, Size ignored_map_index=std::numeric_limits< Size >::max()) const
Fill result with indices of all features within the specified boundaries.
Management and storage of parameters / INI files.
Definition: Param.h:74
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
RealType variance2_
Definition: AsymmetricStatistics.h:144
Compare functor scoring the spectral contrast angle for similarity measurement.
Definition: BinnedSpectralContrastAngle.h:57
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:103
File is empty.
Definition: Exception.h:594
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
const std::vector< DataProcessing > & getDataProcessing() const
returns a const reference to the description of the applied data processing
String suffix(SizeType length) const
returns the suffix of length length
IntensityType getIntensity() const
Definition: Peak1D.h:108
Stores a set of features, together with a 2D tree for fast search.
Definition: KDTreeFeatureMaps.h:49
Base::RealType RealType
Definition: AsymmetricStatistics.h:63
RealT RealType
The real type specified as template argument.
Definition: BasicStatistics.h:74
static constexpr const float DEFAULT_BIN_OFFSET_HIRES
default bin offset for high-resolution data (adapted from doi:10.1007/s13361-015-1179-x)
Definition: BinnedSpectrum.h:102
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications