MSChromatogram#

class pyopenms.MSChromatogram(*args, **kwargs)#

Bases: MSChromatogram

__init__(*args, **kwargs)#

Overload:

__init__(self) None

Overload:

__init__(self, in_0: MSChromatogram) None

Methods

__init__(*args, **kwargs)

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_df([export_meta_values])

Returns a DataFrame representation of the MSChromatogram.

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) 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: bytes | str | String) 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) bytes | str | String#

Returns the name

getNativeID(self) 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_df(export_meta_values: bool = True) DataFrame#

Returns a DataFrame representation of the MSChromatogram.

time: The retention time (in seconds) of the chromatographic peaks. intensity: The intensity (abundance) of the signal at each time point. chromatogram_type: The type of chromatogram. precursor_mz: The mass-to-charge of the precursor ion. precursor_charge: The charge of the precursor ion. comment: A comment assigned to the chromatogram. native_id: The chromatogram native identifier.

Args:

export_meta_values (bool): Whether to export meta values.

Returns:

pd.DataFrame: DataFrame representation of the MSChromatogram.

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: 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: 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: 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: bytes | str | String, in_1: int | float | bytes | str | List[int] | List[float] | List[bytes]) None#

Sets the DataValue corresponding to a name

setName(self, in_0: bytes | str | String) None#

Sets the name

setNativeID(self, native_id: 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#