|
OpenMS
2.6.0
|
Go to the documentation of this file.
42 #define DEBUG_PEAK_PICKING
43 #undef DEBUG_PEAK_PICKING
48 class OnDiscMSExperiment;
120 void pick(
const MSSpectrum& input,
MSSpectrum& output, std::vector<PeakBoundary>& boundaries,
bool check_spacings =
true)
const;
130 void pick(
const MSChromatogram& input,
MSChromatogram& output, std::vector<PeakBoundary>& boundaries,
bool check_spacings =
false)
const;
141 void pickExperiment(
const PeakMap& input,
PeakMap& output,
const bool check_spectrum_type =
true)
const;
154 void pickExperiment(
const PeakMap& input,
156 std::vector<std::vector<PeakBoundary> >& boundaries_spec,
157 std::vector<std::vector<PeakBoundary> >& boundaries_chrom,
158 const bool check_spectrum_type =
true)
const;
171 template <
typename ContainerType>
172 void pick_(
const ContainerType& input, ContainerType& output, std::vector<PeakBoundary>& boundaries,
bool check_spacings =
true)
const;
196 void updateMembers_()
override;
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:88
SpectrumSettings::SpectrumType getType(const bool query_data) const
Determine if spectrum is profile or centroided using up to three layers of information.
centroid data or stick data
Definition: SpectrumSettings.h:73
Base class for TOPP applications.
Definition: TOPPBase.h:144
double mz_max
Definition: PeakPickerHiRes.h:88
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
double spacing_difference_gap_
Definition: PeakPickerHiRes.h:178
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.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
void pickExperiment(const PeakMap &input, PeakMap &output, const bool check_spectrum_type=true) const
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in ...
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static bool contains(const std::vector< T > &container, const E &elem)
Checks whether the element elem is contained in the given container.
Definition: ListUtils.h:146
structure for peak boundaries
Definition: PeakPickerHiRes.h:85
bool report_FWHM_
add floatDataArray 'FWHM'/'FWHM_ppm' to spectra with peak FWHM
Definition: PeakPickerHiRes.h:190
#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
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
UInt getMSLevel() const
Returns the MS level.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:73
bool report_FWHM_as_ppm_
unit of 'FWHM' float data array (can be absolute or ppm).
Definition: PeakPickerHiRes.h:193
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
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...
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:68
Peak picking (conversion from raw to peak data)
Definition: DataProcessing.h:67
double mz_min
Definition: PeakPickerHiRes.h:87
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
double signal_to_noise_
Definition: PeakPickerHiRes.h:175
bool empty() const
Definition: MSExperiment.h:137
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
unsigned missing_
Definition: PeakPickerHiRes.h:184
MSChromatogram & getChromatogram(Size id)
returns a single chromatogram
std::vector< Int > ms_levels_
Definition: PeakPickerHiRes.h:187
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
Management and storage of parameters / INI files.
Definition: Param.h:73
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
double spacing_difference_
Definition: PeakPickerHiRes.h:181
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!