OpenMS  3.0.0
FIAMSDataProcessor.h
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32 // $Authors: Svetlana Kutuzova, Douglas McCloskey $
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34 
35 #pragma once
38 #include <OpenMS/FORMAT/MzTab.h>
39 #include <OpenMS/FORMAT/MzTabM.h>
41 #include <OpenMS/FORMAT/MzMLFile.h>
42 
43 namespace OpenMS
44 {
60  class OPENMS_DLLAPI FIAMSDataProcessor :
61  public DefaultParamHandler
62  {
63 public:
66 
68  ~FIAMSDataProcessor() override = default;
69 
71  FIAMSDataProcessor(const FIAMSDataProcessor& cp) = default;
72 
74  FIAMSDataProcessor& operator=(const FIAMSDataProcessor& fdp) = default;
75 
96  bool run(const MSExperiment& experiment, const float n_seconds, OpenMS::MzTab& output, const bool load_cached_spectrum = true);
97 
105  void cutForTime(const MSExperiment& experiment, const float n_seconds, std::vector<MSSpectrum>& output);
106 
117  MSSpectrum mergeAlongTime(const std::vector<OpenMS::MSSpectrum>& input);
118 
125  MSSpectrum extractPeaks(const MSSpectrum& input);
126 
135  FeatureMap convertToFeatureMap(const MSSpectrum& input);
136 
145  MSSpectrum trackNoise(const MSSpectrum& input);
146 
155  void runAccurateMassSearch(FeatureMap& input, OpenMS::MzTab& output);
156 
160  const std::vector<float>& getMZs();
161 
165  const std::vector<float>& getBinSizes();
166 
167 protected:
168  void updateMembers_() override;
169 
170 private:
174  void storeSpectrum_(const MSSpectrum& input, String filename);
175 
176  std::vector<float> mzs_;
177  std::vector<float> bin_sizes_;
180  };
181 } // namespace OpenMS
MzTabFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::TextFile::addLine
void addLine(const StringType &line)
Definition: TextFile.h:112
TextFile.h
OpenMS::String::fillLeft
String & fillLeft(char c, UInt size)
Adds c on the left side until the size of the string is size.
Size
MzTabM.h
OpenMS::toString
const std::string & toString(const DriftTimeUnit value)
OpenMS::FIAMSDataProcessor::sgfilter_
SavitzkyGolayFilter sgfilter_
Definition: FIAMSDataProcessor.h:178
OpenMS::FIAMSDataProcessor::mzs_
std::vector< float > mzs_
Definition: FIAMSDataProcessor.h:176
OpenMS::FIAMSDataProcessor::picker_
PeakPickerHiRes picker_
Definition: FIAMSDataProcessor.h:179
OpenMS::FeatureMap::sortByIntensity
void sortByIntensity(bool reverse=false)
Sorts the peaks according to ascending intensity.
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name, const DataValue &default_value=DataValue::EMPTY) const
Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not fo...
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
Feature.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
OpenMS::DBoundingBox::encloses
bool encloses(const PositionType &position) const
Checks whether this range contains a certain point.
Definition: DBoundingBox.h:159
FeatureXMLFile.h
OpenMS::MzTab
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:477
StatisticFunctions.h
OpenMS::Peak2D::getIntensity
IntensityType getIntensity() const
Definition: Peak2D.h:166
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::String::number
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
SavitzkyGolayFilter.h
OpenMS::PeakPickerHiRes
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:81
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
FeatureMap.h
OpenMS::BaseFeature::getCharge
const ChargeType & getCharge() const
Non-mutable access to charge state.
MzTab.h
OpenMS::Math
Math namespace.
Definition: BilinearInterpolation.h:42
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::Peak2D::getRT
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::FIAMSDataProcessor
Data processing for FIA-MS data.
Definition: FIAMSDataProcessor.h:60
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::Feature::getConvexHull
ConvexHull2D & getConvexHull() const
Returns the overall convex hull of the feature (calculated from the convex hulls of the mass traces)
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
OpenMS::Peak2D::getPosition
const PositionType & getPosition() const
Non-mutable access to the position.
Definition: Peak2D.h:178
OpenMS::ConvexHull2D::getBoundingBox
DBoundingBox< 2 > getBoundingBox() const
returns the bounding box of the feature hull points
OpenMS::TextFile::store
void store(const String &filename)
Writes the data to a file.
OpenMS::FIAMSDataProcessor::bin_sizes_
std::vector< float > bin_sizes_
Definition: FIAMSDataProcessor.h:177
OpenMS::SavitzkyGolayFilter
Computes the Savitzky-Golay filter coefficients using QR decomposition.
Definition: SavitzkyGolayFilter.h:101
OpenMS::Peak2D::getMZ
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
PeakPickerHiRes.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::FeatureMap::sortByPosition
void sortByPosition()
Sort features by position. Lexicographical comparison (first RT then m/z) is done.
TOPPBase.h
OpenMS::Math::pearsonCorrelationCoefficient
static double pearsonCorrelationCoefficient(IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)
Calculates the Pearson correlation coefficient for the values in [begin_a, end_a) and [begin_b,...
Definition: StatisticFunctions.h:521