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OpenMS
2.6.0
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95 bool run(
const MSExperiment& experiment,
const float n_seconds,
OpenMS::MzTab& output,
const bool load_cached_spectrum =
true);
104 void cutForTime(
const MSExperiment& experiment,
const float n_seconds, std::vector<MSSpectrum>& output);
116 MSSpectrum mergeAlongTime(
const std::vector<OpenMS::MSSpectrum>& input);
159 const std::vector<float>& getMZs();
164 const std::vector<float>& getBinSizes();
167 void updateMembers_()
override;
Base class for TOPP applications.
Definition: TOPPBase.h:144
void addLine(const StringType &line)
Definition: TextFile.h:112
String & fillLeft(char c, UInt size)
Adds c on the left side until the size of the string is size.
SavitzkyGolayFilter sgfilter_
Definition: FIAMSDataProcessor.h:177
std::vector< float > mzs_
Definition: FIAMSDataProcessor.h:175
PeakPickerHiRes picker_
Definition: FIAMSDataProcessor.h:178
void sortByIntensity(bool reverse=false)
Sorts the peaks according to ascending intensity.
bool has(const Key &key) const
Test whether the map contains the given key.
Definition: Map.h:108
A more convenient string class.
Definition: String.h:59
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
bool encloses(const PositionType &position) const
Checks whether this range contains a certain point.
Definition: DBoundingBox.h:159
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:800
IntensityType getIntensity() const
Definition: Peak2D.h:166
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:73
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
const ChargeType & getCharge() const
Non-mutable access to charge state.
Math namespace.
Definition: BilinearInterpolation.h:42
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
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Data processing for FIA-MS data.
Definition: FIAMSDataProcessor.h:59
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
String toString(const T &i)
fallback template for general purpose using Boost::Karma; more specializations below
Definition: StringUtils.h:127
A container for features.
Definition: FeatureMap.h:97
ConvexHull2D & getConvexHull() const
Returns the overall convex hull of the feature (calculated from the convex hulls of the mass traces)
An LC-MS feature.
Definition: Feature.h:70
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
const PositionType & getPosition() const
Non-mutable access to the position.
Definition: Peak2D.h:178
DBoundingBox< 2 > getBoundingBox() const
returns the bounding box of the feature hull points
void store(const String &filename)
Writes the data to a file.
std::vector< float > bin_sizes_
Definition: FIAMSDataProcessor.h:176
Computes the Savitzky-Golay filter coefficients using QR decomposition.
Definition: SavitzkyGolayFilter.h:101
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
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
void sortByPosition()
Sort features by position. Lexicographical comparison (first RT then m/z) is done.
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:505