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OpenMS
2.5.0
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Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:88
void filterExperiment(PeakMap &map)
Removed the noise from an MSExperiment containing profile data.
Definition: SavitzkyGolayFilter.h:214
RETURN_STATUS
Definition: NonNegativeLeastSquaresSolver.h:50
centroid data or stick data
Definition: SpectrumSettings.h:73
Base class for TOPP applications.
Definition: TOPPBase.h:144
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
bool isSorted() const
Checks if all peaks are sorted with respect to ascending RT.
void filterExperiment(PeakMap &map)
Smoothes an MSExperiment containing profile data.
Definition: GaussFilter.h:193
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:58
void filter(MSSpectrum &spectrum)
Smoothes an MSSpectrum containing profile data.
Definition: GaussFilter.h:92
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
Wrapper for a non-negative least squares (NNLS) solver.
Definition: NonNegativeLeastSquaresSolver.h:46
#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
Size size() const
Definition: MSExperiment.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
const std::vector< MSChromatogram > & getChromatograms() const
returns the chromatogram 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...
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
Smoothing of the signal to reduce noise.
Definition: DataProcessing.h:63
void filter(InputIt first, InputIt last, OutputIt d_first)
Definition: SavitzkyGolayFilter.h:115
MSChromatogram & getChromatogram(Size id)
returns a single chromatogram
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false)
Transforms a map while loading using the supplied MSDataConsumer.
The representation of a chromatogram.
Definition: MSChromatogram.h:54
const char * getMessage() const noexcept
Returns the message.
Management and storage of parameters / INI files.
Definition: Param.h:73
Computes the Savitzky-Golay filter coefficients using QR decomposition.
Definition: SavitzkyGolayFilter.h:101
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
Definition: NonNegativeLeastSquaresSolver.h:52
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform prof...
Definition: GaussFilter.h:74