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OpenMS
2.4.0
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80 float operator()(
const std::pair<float, float> & a,
const std::pair<float, float> & b)
const;
88 float operator()(
const std::pair<float, float> &
c)
const;
98 void setScale(
float x);
Base class for TOPP applications.
Definition: TOPPBase.h:150
Implements the isotope wavelet feature finder.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:59
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:119
float scale_
Definition: EuclideanSimilarity.h:55
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
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
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
IntensityType getIntensity() const
Definition: Peak2D.h:166
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:110
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
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...
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
The main feature finder class.
Definition: FeatureFinder.h:56
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getParameters() const
Non-mutable access to the parameters.
CompareFunctor for 2Dpoints.
Definition: EuclideanSimilarity.h:51
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
A container for consensus elements.
Definition: ConsensusMap.h:75
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
A container for features.
Definition: FeatureMap.h:93
An LC-MS feature.
Definition: Feature.h:70
Iterator end()
Definition: MSExperiment.h:167
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
void getPrimaryMSRunPath(StringList &toFill) const
get the file path to the first MS run
void updateRanges() override
Updates minimum and maximum position/intensity.
Management and storage of parameters / INI files.
Definition: Param.h:74
No progress logging.
Definition: ProgressLogger.h:74
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
const double NEUTRON_MASS_U
void run(const String &algorithm_name, PeakMap &input_map, FeatureMap &features, const Param ¶m, const FeatureMap &seeds)
Executes the FeatureFinder using the given algorithm.
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:103
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
void setRT(double rt)
Sets the absolute retention time (in seconds)
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
void setPrimaryMSRunPath(const StringList &s)
set the file paths to the primary MS run (stored in ColumnHeaders)
static double absdev(IteratorType begin, IteratorType end, double mean=std::numeric_limits< double >::max())
Calculates the absolute deviation of a range of values.
Definition: StatisticFunctions.h:321
void insert(const ConsensusFeature &cf)
Adds all feature handles (of the CF) into the consensus feature.
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61