MSChromatogram

class pyopenms.MSChromatogram

Bases: object

Cython implementation of _MSChromatogram

Original C++ documentation is available here: – Inherits from [‘ChromatogramSettings’, ‘RangeManagerRtInt’]

The representation of a chromatogram. 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(ChromatogramSettings) for information about meta-information

Usage:

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: MSChromatogram) → None

Methods

`__init__`	Overload:
`clear`(self, in_0)	Clears all data and meta data
`clearMetaInfo`(self)	Removes all meta values
`clearRanges`(self)	Resets all range dimensions as empty
`findNearest`(self, in_0)	Binary search for the peak nearest to a specific RT :note: Make sure the chromatogram is sorted with respect to RT! Otherwise the result is undefined
`getAcquisitionInfo`(self)	Returns the acquisition info
`getChromatogramType`(self)	Get the chromatogram type
`getComment`(self)	Returns the free-text comment
`getDataProcessing`(self)	Returns the description of the applied processing
`getFloatDataArrays`(self)	Returns a reference to the float meta data arrays
`getInstrumentSettings`(self)	Returns the instrument settings of the current spectrum
`getIntegerDataArrays`(self)	Returns a reference to the integer meta data arrays
`getKeys`(self, keys)	Fills the given vector with a list of all keys for which a value is set
`getMZ`(self)	Returns the mz of the product entry, makes sense especially for MRM scans
`getMaxIntensity`(self)	Returns the maximum intensity
`getMaxRT`(self)	Returns the maximum RT
`getMetaValue`(self, in_0)	Returns the value corresponding to a string, or
`getMinIntensity`(self)	Returns the minimum intensity
`getMinRT`(self)	Returns the minimum RT
`getName`(self)	Returns the name
`getNativeID`(self)	Returns the native identifier for the spectrum, used by the acquisition software.
`getPrecursor`(self)	Returns the precursors
`getProduct`(self)	Returns the product ion
`getSourceFile`(self)	Returns the source file
`getStringDataArrays`(self)	Returns a reference to the string meta data arrays
`get_peaks`
`isMetaEmpty`(self)	Returns if the MetaInfo is empty
`isSorted`(self)	Checks if all peaks are sorted with respect to ascending RT
`metaRegistry`(self)	Returns a reference to the MetaInfoRegistry
`metaValueExists`(self, in_0)	Returns whether an entry with the given name exists
`push_back`(self, in_0)	Append a peak
`removeMetaValue`(self, in_0)	Removes the DataValue corresponding to name if it exists
`reserve`(self, n)
`resize`(self, n)	Resize the peak array
`setAcquisitionInfo`(self, acquisition_info)	Sets the acquisition info
`setChromatogramType`(self, type)	Sets the chromatogram type
`setComment`(self, comment)	Sets the free-text comment
`setDataProcessing`(self, in_0)	Sets the description of the applied processing
`setFloatDataArrays`(self, fda)	Sets the float meta data arrays
`setInstrumentSettings`(self, instrument_settings)	Sets the instrument settings of the current spectrum
`setIntegerDataArrays`(self, ida)	Sets the integer meta data arrays
`setMetaValue`(self, in_0, in_1)	Sets the DataValue corresponding to a name
`setName`(self, in_0)	Sets the name
`setNativeID`(self, native_id)	Sets the native identifier for the spectrum, used by the acquisition software.
`setPrecursor`(self, precursor)	Sets the precursors
`setProduct`(self, p)	Sets the product ion
`setSourceFile`(self, source_file)	Sets the source file
`setStringDataArrays`(self, sda)	Sets the string meta data arrays
`set_peaks`
`size`(self)
`sortByIntensity`(self, reverse)	Lexicographically sorts the peaks by their intensity
`sortByPosition`(self)	Lexicographically sorts the peaks by their position
`updateRanges`(self)

clear(self, in_0: int) → None

Clears all data and meta data

Parameters: clear_meta_data – If true, all meta data is cleared in addition to the data

clearMetaInfo(self) → None: Removes all meta values

clearRanges(self) → None: Resets all range dimensions as empty

findNearest(self, in_0: float) → int

Binary search for the peak nearest to a specific RT :note: Make sure the chromatogram is sorted with respect to RT! Otherwise the result is undefined

Parameters: rt – The searched for mass-to-charge ratio searched
Returns: Returns the index of the peak.
Raises: Exception: Precondition is thrown if the chromatogram is empty (not only in debug mode)

getAcquisitionInfo(self) → AcquisitionInfo: Returns the acquisition info

getChromatogramType(self) → int: Get the chromatogram type

getComment(self) → Union[bytes, str, String]: Returns the free-text comment

getDataProcessing(self) → List[DataProcessing]: Returns the description of the applied processing

getFloatDataArrays(self) → List[FloatDataArray]: Returns a reference to the float meta data arrays

getInstrumentSettings(self) → InstrumentSettings: Returns the instrument settings of the current spectrum

getIntegerDataArrays(self) → List[IntegerDataArray]: Returns a reference to the integer meta data arrays

getKeys(self, keys: List[bytes]) → None: Fills the given vector with a list of all keys for which a value is set

getMZ(self) → float: Returns the mz of the product entry, makes sense especially for MRM scans

getMaxIntensity(self) → float: Returns the maximum intensity

getMaxRT(self) → float: Returns the maximum RT

getMetaValue(self, in_0: Union[bytes, str, String]) → Union[int, float, bytes, str, List[int], List[float], List[bytes]]: Returns the value corresponding to a string, or

getMinIntensity(self) → float: Returns the minimum intensity

getMinRT(self) → float: Returns the minimum RT

getName(self) → Union[bytes, str, String]: Returns the name

getNativeID(self) → Union[bytes, str, String]: Returns the native identifier for the spectrum, used by the acquisition software.

getPrecursor(self) → Precursor: Returns the precursors

getProduct(self) → Product: Returns the product ion

getSourceFile(self) → SourceFile: Returns the source file

getStringDataArrays(self) → List[StringDataArray]: Returns a reference to the string meta data arrays

get_peaks()

isMetaEmpty(self) → bool: Returns if the MetaInfo is empty

isSorted(self) → bool: Checks if all peaks are sorted with respect to ascending RT

metaRegistry(self) → MetaInfoRegistry: Returns a reference to the MetaInfoRegistry

metaValueExists(self, in_0: Union[bytes, str, String]) → bool: Returns whether an entry with the given name exists

push_back(self, in_0: ChromatogramPeak) → None: Append a peak

removeMetaValue(self, in_0: Union[bytes, str, String]) → None: Removes the DataValue corresponding to name if it exists

reserve(self, n: int) → None

resize(self, n: int) → None: Resize the peak array

setAcquisitionInfo(self, acquisition_info: AcquisitionInfo) → None: Sets the acquisition info

setChromatogramType(self, type: int) → None: Sets the chromatogram type

setComment(self, comment: Union[bytes, str, String]) → None: Sets the free-text comment

setDataProcessing(self, in_0: List[DataProcessing]) → None: Sets the description of the applied processing

setFloatDataArrays(self, fda: List[FloatDataArray]) → None: Sets the float meta data arrays

setInstrumentSettings(self, instrument_settings: InstrumentSettings) → None: Sets the instrument settings of the current spectrum

setIntegerDataArrays(self, ida: List[IntegerDataArray]) → None: Sets the integer meta data arrays

setMetaValue(self, in_0: Union[bytes, str, String], in_1: Union[int, float, bytes, str, List[int], List[float], List[bytes]]) → None: Sets the DataValue corresponding to a name

setName(self, in_0: Union[bytes, str, String]) → None: Sets the name

setNativeID(self, native_id: Union[bytes, str, String]) → None: Sets the native identifier for the spectrum, used by the acquisition software.

setPrecursor(self, precursor: Precursor) → None: Sets the precursors

setProduct(self, p: Product) → None: Sets the product ion

setSourceFile(self, source_file: SourceFile) → None: Sets the source file

setStringDataArrays(self, sda: List[StringDataArray]) → None: Sets the string meta data arrays

set_peaks()

size(self) → int

sortByIntensity(self, reverse: bool) → None

Lexicographically sorts the peaks by their intensity

Sorts the peaks according to ascending intensity. Meta data arrays will be sorted accordingly

sortByPosition(self) → None

Lexicographically sorts the peaks by their position

The chromatogram is sorted with respect to position. Meta data arrays will be sorted accordingly

updateRanges(self) → None