MSSpectrum

class pyopenms.Plotting.MSSpectrum

Bases: object

Cython implementation of _MSSpectrum

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1MSSpectrum.html

– Inherits from [‘SpectrumSettings’, ‘RangeManagerMzInt’]

The representation of a 1D spectrum. Raw data access is proved by get_peaks and set_peaks, which yields numpy arrays Iterations yields access to underlying peak objects but is slower Extra data arrays can be accessed through getFloatDataArrays / getIntegerDataArrays / getStringDataArrays See help(SpectrumSettings) for information about meta-information —– Usage:

ms_level = spectrum.getMSLevel() rt = spectrum.getRT() mz, intensities = spectrum.get_peaks()

__init__()

Cython signature: void MSSpectrum()
Cython signature: void MSSpectrum(MSSpectrum &)

Methods

`__init__`	Cython signature: void MSSpectrum()
`calculateTIC`	Cython signature: double calculateTIC() Returns the total ion current (=sum) of peak intensities in the spectrum
`clear`	Cython signature: void clear(bool clear_meta_data) Clears all data (and meta data if clear_meta_data is true)
`clearMetaInfo`	Cython signature: void clearMetaInfo() Removes all meta values
`clearRanges`	Cython signature: void clearRanges() Resets all range dimensions as empty
`containsIMData`	Cython signature: bool containsIMData()
`findHighestInWindow`	Cython signature: int findHighestInWindow(double mz, double tolerance_left, double tolerance_right) Returns the index of the highest peak in the provided abs.
`findNearest`	Cython signature: int findNearest(double mz)
`getAcquisitionInfo`	Cython signature: AcquisitionInfo getAcquisitionInfo() Returns a const reference to the acquisition info
`getComment`	Cython signature: String getComment() Returns the free-text comment
`getDataProcessing`	Cython signature: libcpp_vector[shared_ptr[DataProcessing]] getDataProcessing()
`getDriftTime`	Cython signature: double getDriftTime() Returns the drift time (-1 if not set)
`getDriftTimeUnit`	Cython signature: DriftTimeUnit getDriftTimeUnit()
`getDriftTimeUnitAsString`	Cython signature: String getDriftTimeUnitAsString()
`getFloatDataArrays`	Cython signature: libcpp_vector[FloatDataArray] getFloatDataArrays() Returns the additional float data arrays to store e.g.
`getIMData`
`getInstrumentSettings`	Cython signature: InstrumentSettings getInstrumentSettings() Returns a const reference to the instrument settings of the current spectrum
`getIntegerDataArrays`	Cython signature: libcpp_vector[IntegerDataArray] getIntegerDataArrays() Returns the additional int data arrays to store e.g.
`getKeys`	Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
`getMSLevel`	Cython signature: unsigned int getMSLevel() Returns the MS level
`getMaxIntensity`	Cython signature: double getMaxIntensity() Returns the maximum intensity
`getMaxMZ`	Cython signature: double getMaxMZ() Returns the maximum m/z
`getMetaValue`	Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
`getMinIntensity`	Cython signature: double getMinIntensity() Returns the minimum intensity
`getMinMZ`	Cython signature: double getMinMZ() Returns the minimum m/z
`getName`	Cython signature: String getName()
`getNativeID`	Cython signature: String getNativeID() Returns the native identifier for the spectrum, used by the acquisition software
`getPeptideIdentifications`	Cython signature: libcpp_vector[PeptideIdentification] getPeptideIdentifications() Returns a const reference to the PeptideIdentification vector
`getPrecursors`	Cython signature: libcpp_vector[Precursor] getPrecursors() Returns a const reference to the precursors
`getProducts`	Cython signature: libcpp_vector[Product] getProducts() Returns a const reference to the products
`getRT`	Cython signature: double getRT() Returns the absolute retention time (in seconds)
`getSourceFile`	Cython signature: SourceFile getSourceFile() Returns a const reference to the source file
`getStringDataArrays`	Cython signature: libcpp_vector[StringDataArray] getStringDataArrays() Returns the additional string data arrays to store e.g.
`getType`	Cython signature: int getType() Returns the spectrum type (centroided (PEAKS) or profile data (RAW))
`get_peaks`	Cython signature: numpy_vector, numpy_vector get_peaks()
`intensityInRange`
`isMetaEmpty`	Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
`isSorted`	Cython signature: bool isSorted() Returns true if the spectrum is sorte by m/z
`metaRegistry`	Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
`metaValueExists`	Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
`push_back`	Cython signature: void push_back(Peak1D) Append a peak
`removeMetaValue`	Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
`reserve`	Cython signature: void reserve(size_t n)
`resize`	Cython signature: void resize(size_t n) Resize the peak array
`select`	Cython signature: MSSpectrum select(libcpp_vector[size_t] & indices) Subset the spectrum by indices.
`setAcquisitionInfo`	Cython signature: void setAcquisitionInfo(AcquisitionInfo) Sets the acquisition info
`setComment`	Cython signature: void setComment(String) Sets the free-text comment
`setDataProcessing`	Cython signature: void setDataProcessing(libcpp_vector[shared_ptr[DataProcessing]])
`setDriftTime`	Cython signature: void setDriftTime(double) Sets the drift time (-1 if not set)
`setDriftTimeUnit`	Cython signature: void setDriftTimeUnit(DriftTimeUnit dt)
`setFloatDataArrays`	Cython signature: void setFloatDataArrays(libcpp_vector[FloatDataArray] fda) Sets the additional float data arrays to store e.g.
`setInstrumentSettings`	Cython signature: void setInstrumentSettings(InstrumentSettings) Sets the instrument settings of the current spectrum
`setIntegerDataArrays`	Cython signature: void setIntegerDataArrays(libcpp_vector[IntegerDataArray] ida) Sets the additional int data arrays to store e.g.
`setMSLevel`	Cython signature: void setMSLevel(unsigned int) Sets the MS level
`setMetaValue`	Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
`setName`	Cython signature: void setName(String)
`setNativeID`	Cython signature: void setNativeID(String) Sets the native identifier for the spectrum, used by the acquisition software
`setPeptideIdentifications`	Cython signature: void setPeptideIdentifications(libcpp_vector[PeptideIdentification]) Sets the PeptideIdentification vector
`setPrecursors`	Cython signature: void setPrecursors(libcpp_vector[Precursor]) Sets the precursors
`setProducts`	Cython signature: void setProducts(libcpp_vector[Product]) Sets the products
`setRT`	Cython signature: void setRT(double) Sets the absolute retention time (in seconds)
`setSourceFile`	Cython signature: void setSourceFile(SourceFile) Sets the source file
`setStringDataArrays`	Cython signature: void setStringDataArrays(libcpp_vector[StringDataArray] sda) Sets the additional string data arrays to store e.g.
`setType`	Cython signature: void setType(SpectrumType) Sets the spectrum type
`set_peaks`	Cython signature: set_peaks((numpy_vector, numpy_vector))
`size`	Cython signature: size_t size() Returns the number of peaks in the spectrum
`sortByIntensity`	Cython signature: void sortByIntensity(bool reverse)
`sortByPosition`	Cython signature: void sortByPosition()
`unify`	Cython signature: void unify(SpectrumSettings)
`updateRanges`	Cython signature: void updateRanges()

calculateTIC(): Cython signature: double calculateTIC() Returns the total ion current (=sum) of peak intensities in the spectrum

clear(): Cython signature: void clear(bool clear_meta_data) Clears all data (and meta data if clear_meta_data is true)

clearMetaInfo(): Cython signature: void clearMetaInfo() Removes all meta values

clearRanges(): Cython signature: void clearRanges() Resets all range dimensions as empty

containsIMData(): Cython signature: bool containsIMData()

findHighestInWindow(): Cython signature: int findHighestInWindow(double mz, double tolerance_left, double tolerance_right) Returns the index of the highest peak in the provided abs. m/z tolerance window to the left and right (-1 if none match)

findNearest()

Cython signature: int findNearest(double mz) Returns the index of the closest peak in m/z
Cython signature: int findNearest(double mz, double tolerance) Returns the index of the closest peak in the provided +/- m/z tolerance window (-1 if none match)
Cython signature: int findNearest(double mz, double tolerance_left, double tolerance_right) Returns the index of the closest peak in the provided abs. m/z tolerance window to the left and right (-1 if none match)

getAcquisitionInfo(): Cython signature: AcquisitionInfo getAcquisitionInfo() Returns a const reference to the acquisition info

getComment(): Cython signature: String getComment() Returns the free-text comment

getDataProcessing(): Cython signature: libcpp_vector[shared_ptr[DataProcessing]] getDataProcessing()

getDriftTime(): Cython signature: double getDriftTime() Returns the drift time (-1 if not set)

getDriftTimeUnit(): Cython signature: DriftTimeUnit getDriftTimeUnit()

getDriftTimeUnitAsString(): Cython signature: String getDriftTimeUnitAsString()

getFloatDataArrays(): Cython signature: libcpp_vector[FloatDataArray] getFloatDataArrays() Returns the additional float data arrays to store e.g. meta data

getIMData()

getInstrumentSettings(): Cython signature: InstrumentSettings getInstrumentSettings() Returns a const reference to the instrument settings of the current spectrum

getIntegerDataArrays(): Cython signature: libcpp_vector[IntegerDataArray] getIntegerDataArrays() Returns the additional int data arrays to store e.g. meta data

getKeys(): Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set

getMSLevel(): Cython signature: unsigned int getMSLevel() Returns the MS level

getMaxIntensity(): Cython signature: double getMaxIntensity() Returns the maximum intensity

getMaxMZ(): Cython signature: double getMaxMZ() Returns the maximum m/z

getMetaValue(): Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or

getMinIntensity(): Cython signature: double getMinIntensity() Returns the minimum intensity

getMinMZ(): Cython signature: double getMinMZ() Returns the minimum m/z

getName(): Cython signature: String getName()

getNativeID(): Cython signature: String getNativeID() Returns the native identifier for the spectrum, used by the acquisition software

getPeptideIdentifications(): Cython signature: libcpp_vector[PeptideIdentification] getPeptideIdentifications() Returns a const reference to the PeptideIdentification vector

getPrecursors(): Cython signature: libcpp_vector[Precursor] getPrecursors() Returns a const reference to the precursors

getProducts(): Cython signature: libcpp_vector[Product] getProducts() Returns a const reference to the products

getRT(): Cython signature: double getRT() Returns the absolute retention time (in seconds)

getSourceFile(): Cython signature: SourceFile getSourceFile() Returns a const reference to the source file

getStringDataArrays(): Cython signature: libcpp_vector[StringDataArray] getStringDataArrays() Returns the additional string data arrays to store e.g. meta data

getType(): Cython signature: int getType() Returns the spectrum type (centroided (PEAKS) or profile data (RAW))

get_peaks()

Cython signature: numpy_vector, numpy_vector get_peaks()

Will return a tuple of two numpy arrays (m/z, intensity) corresponding to the peaks in the MSSpectrum. Provides fast access to peaks.

intensityInRange()

isMetaEmpty(): Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty

isSorted(): Cython signature: bool isSorted() Returns true if the spectrum is sorte by m/z

metaRegistry(): Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry

metaValueExists(): Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists

push_back(): Cython signature: void push_back(Peak1D) Append a peak

removeMetaValue(): Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists

reserve(): Cython signature: void reserve(size_t n)

resize(): Cython signature: void resize(size_t n) Resize the peak array

select(): Cython signature: MSSpectrum select(libcpp_vector[size_t] & indices) Subset the spectrum by indices. Also applies to associated data arrays if present.

setAcquisitionInfo(): Cython signature: void setAcquisitionInfo(AcquisitionInfo) Sets the acquisition info

setComment(): Cython signature: void setComment(String) Sets the free-text comment

setDataProcessing(): Cython signature: void setDataProcessing(libcpp_vector[shared_ptr[DataProcessing]])

setDriftTime(): Cython signature: void setDriftTime(double) Sets the drift time (-1 if not set)

setDriftTimeUnit(): Cython signature: void setDriftTimeUnit(DriftTimeUnit dt)

setFloatDataArrays(): Cython signature: void setFloatDataArrays(libcpp_vector[FloatDataArray] fda) Sets the additional float data arrays to store e.g. meta data

setInstrumentSettings(): Cython signature: void setInstrumentSettings(InstrumentSettings) Sets the instrument settings of the current spectrum

setIntegerDataArrays(): Cython signature: void setIntegerDataArrays(libcpp_vector[IntegerDataArray] ida) Sets the additional int data arrays to store e.g. meta data

setMSLevel(): Cython signature: void setMSLevel(unsigned int) Sets the MS level

setMetaValue(): Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name

setName(): Cython signature: void setName(String)

setNativeID(): Cython signature: void setNativeID(String) Sets the native identifier for the spectrum, used by the acquisition software

setPeptideIdentifications(): Cython signature: void setPeptideIdentifications(libcpp_vector[PeptideIdentification]) Sets the PeptideIdentification vector

setPrecursors(): Cython signature: void setPrecursors(libcpp_vector[Precursor]) Sets the precursors

setProducts(): Cython signature: void setProducts(libcpp_vector[Product]) Sets the products

setRT(): Cython signature: void setRT(double) Sets the absolute retention time (in seconds)

setSourceFile(): Cython signature: void setSourceFile(SourceFile) Sets the source file

setStringDataArrays(): Cython signature: void setStringDataArrays(libcpp_vector[StringDataArray] sda) Sets the additional string data arrays to store e.g. meta data

setType(): Cython signature: void setType(SpectrumType) Sets the spectrum type

set_peaks()

Cython signature: set_peaks((numpy_vector, numpy_vector))

Takes a tuple or list of two arrays (m/z, intensity) and populates the MSSpectrum. The arrays can be numpy arrays (faster).

size(): Cython signature: size_t size() Returns the number of peaks in the spectrum

sortByIntensity(): Cython signature: void sortByIntensity(bool reverse)

sortByPosition(): Cython signature: void sortByPosition()

unify(): Cython signature: void unify(SpectrumSettings)

updateRanges(): Cython signature: void updateRanges()