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