PeakFileOptions

class pyopenms.PeakFileOptions

Bases: object

Cython implementation of _PeakFileOptions

Original C++ documentation is available here

Options for loading files containing peak data

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: PeakFileOptions) → None

Methods

`__init__`	Overload:
`addMSLevel`(self, level)	Adds a desired MS level for peaks to load
`clearMSLevels`(self)	Clears the MS levels
`containsMSLevel`(self, level)	Returns true, if MS level level has been set
`getCompression`(self)	Returns true, if data should be compressed when writing
`getFillData`(self)	Returns whether to fill the actual data into the container (spectrum/chromatogram)
`getForceMQCompatability`(self)	[mzXML only!]Returns Whether to write a scan-index and meta data to indicate a Thermo FTMS/ITMS instrument (required to have parameter control in MQ)
`getForceTPPCompatability`(self)	[mzML only!]Returns Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z
`getIntensity32Bit`(self)	Returns true, if intensity data should be stored with 32bit precision
`getIntensityRange`(self)	Returns the intensity range
`getMSLevels`(self)	Returns the set MS levels
`getMZRange`(self)	Returns the MZ range
`getMaxDataPoolSize`(self)	Returns maximal size of the data pool
`getMetadataOnly`(self)	Returns whether or not to load only meta data
`getMz32Bit`(self)	Returns true, if mz-data and rt-data should be stored with 32bit precision
`getNumpressConfigurationFloatDataArray`(self)	Sets numpress configuration options for float data arrays
`getNumpressConfigurationIntensity`(self)	Sets numpress configuration options for intensity dimension
`getNumpressConfigurationMassTime`(self)	Sets numpress configuration options for m/z or rt dimension
`getRTRange`(self)	Returns the RT range
`getSkipXMLChecks`(self)	Returns whether to skip some XML checks and be fast instead
`getSortChromatogramsByRT`(self)	Returns whether or not peaks in chromatograms should be sorted
`getSortSpectraByMZ`(self)	Returns whether or not peaks in spectra should be sorted
`getWriteIndex`(self)	Returns whether to write an index at the end of the file (e.g.
`getWriteSupplementalData`(self)	Returns whether or not to write supplemental peak data in MzData files
`hasFilters`(self)
`hasIntensityRange`(self)	Returns true if an intensity range has been set
`hasMSLevels`(self)	Returns true, if MS levels have been set
`hasMZRange`(self)	Returns true if an MZ range has been set
`hasRTRange`(self)	Returns true if an RT range has been set
`setCompression`(self, in_0)	Sets if data should be compressed when writing
`setFillData`(self, only)	Sets whether to fill the actual data into the container (spectrum/chromatogram)
`setForceMQCompatability`(self, forceMQ)	[mzXML only!]Returns Whether to write a scan-index and meta data to indicate a Thermo FTMS/ITMS instrument (required to have parameter control in MQ)
`setForceTPPCompatability`(self, forceTPP)	[ mzML only!]Returns Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z
`setIntensity32Bit`(self, int_32_bit)	Sets if intensity data should be stored with 32bit or 64bit precision
`setIntensityRange`(self, range_)	Restricts the range of intensity values for peaks to load
`setMSLevels`(self, levels)	Sets the desired MS levels for peaks to load
`setMZRange`(self, range_)	Restricts the range of MZ values for peaks to load
`setMaxDataPoolSize`(self, s)	Sets maximal size of the data pool
`setMetadataOnly`(self, in_0)	Sets whether or not to load only meta data
`setMz32Bit`(self, mz_32_bit)	Sets if mz-data and rt-data should be stored with 32bit or 64bit precision
`setNumpressConfigurationFloatDataArray`(self, ...)	Returns numpress configuration options for float data arrays
`setNumpressConfigurationIntensity`(self, config)	Returns numpress configuration options for intensity dimension
`setNumpressConfigurationMassTime`(self, config)	Returns numpress configuration options for m/z or rt dimension
`setRTRange`(self, range_)	Restricts the range of RT values for peaks to load
`setSkipXMLChecks`(self, only)	Sets whether to skip some XML checks and be fast instead
`setSortChromatogramsByRT`(self, doSort)	Sets whether or not to sort peaks in chromatograms
`setSortSpectraByMZ`(self, doSort)	Sets whether or not to sort peaks in spectra
`setWriteIndex`(self, write_index)	Returns whether to write an index at the end of the file (e.g.
`setWriteSupplementalData`(self, in_0)	Sets whether or not to write supplemental peak data in MzData files

addMSLevel(self, level: int) → None: Adds a desired MS level for peaks to load

clearMSLevels(self) → None: Clears the MS levels

containsMSLevel(self, level: int) → bool: Returns true, if MS level level has been set

getCompression(self) → bool: Returns true, if data should be compressed when writing

getFillData(self) → bool: Returns whether to fill the actual data into the container (spectrum/chromatogram)

getForceMQCompatability(self) → bool: [mzXML only!]Returns Whether to write a scan-index and meta data to indicate a Thermo FTMS/ITMS instrument (required to have parameter control in MQ)

getForceTPPCompatability(self) → bool: [mzML only!]Returns Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z

getIntensity32Bit(self) → bool: Returns true, if intensity data should be stored with 32bit precision

getIntensityRange(self) → DRange1: Returns the intensity range

getMSLevels(self) → List[int]: Returns the set MS levels

getMZRange(self) → DRange1: Returns the MZ range

getMaxDataPoolSize(self) → int: Returns maximal size of the data pool

getMetadataOnly(self) → bool: Returns whether or not to load only meta data

getMz32Bit(self) → bool: Returns true, if mz-data and rt-data should be stored with 32bit precision

getNumpressConfigurationFloatDataArray(self) → NumpressConfig: Sets numpress configuration options for float data arrays

getNumpressConfigurationIntensity(self) → NumpressConfig: Sets numpress configuration options for intensity dimension

getNumpressConfigurationMassTime(self) → NumpressConfig: Sets numpress configuration options for m/z or rt dimension

getRTRange(self) → DRange1: Returns the RT range

getSkipXMLChecks(self) → bool: Returns whether to skip some XML checks and be fast instead

getSortChromatogramsByRT(self) → bool: Returns whether or not peaks in chromatograms should be sorted

getSortSpectraByMZ(self) → bool: Returns whether or not peaks in spectra should be sorted

getWriteIndex(self) → bool: Returns whether to write an index at the end of the file (e.g. indexedmzML file format)

getWriteSupplementalData(self) → bool: Returns whether or not to write supplemental peak data in MzData files

hasFilters(self) → bool

hasIntensityRange(self) → bool: Returns true if an intensity range has been set

hasMSLevels(self) → bool: Returns true, if MS levels have been set

hasMZRange(self) → bool: Returns true if an MZ range has been set

hasRTRange(self) → bool: Returns true if an RT range has been set

setCompression(self, in_0: bool) → None: Sets if data should be compressed when writing

setFillData(self, only: bool) → None: Sets whether to fill the actual data into the container (spectrum/chromatogram)

setForceMQCompatability(self, forceMQ: bool) → None: [mzXML only!]Returns Whether to write a scan-index and meta data to indicate a Thermo FTMS/ITMS instrument (required to have parameter control in MQ)

setForceTPPCompatability(self, forceTPP: bool) → None: [ mzML only!]Returns Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z

setIntensity32Bit(self, int_32_bit: bool) → None: Sets if intensity data should be stored with 32bit or 64bit precision

setIntensityRange(self, range_: DRange1) → None: Restricts the range of intensity values for peaks to load

setMSLevels(self, levels: List[int]) → None: Sets the desired MS levels for peaks to load

setMZRange(self, range_: DRange1) → None: Restricts the range of MZ values for peaks to load

setMaxDataPoolSize(self, s: int) → None: Sets maximal size of the data pool

setMetadataOnly(self, in_0: bool) → None: Sets whether or not to load only meta data

setMz32Bit(self, mz_32_bit: bool) → None: Sets if mz-data and rt-data should be stored with 32bit or 64bit precision

setNumpressConfigurationFloatDataArray(self, config: NumpressConfig) → None: Returns numpress configuration options for float data arrays

setNumpressConfigurationIntensity(self, config: NumpressConfig) → None: Returns numpress configuration options for intensity dimension

setNumpressConfigurationMassTime(self, config: NumpressConfig) → None: Returns numpress configuration options for m/z or rt dimension

setRTRange(self, range_: DRange1) → None: Restricts the range of RT values for peaks to load

setSkipXMLChecks(self, only: bool) → None: Sets whether to skip some XML checks and be fast instead

setSortChromatogramsByRT(self, doSort: bool) → None: Sets whether or not to sort peaks in chromatograms

setSortSpectraByMZ(self, doSort: bool) → None: Sets whether or not to sort peaks in spectra

setWriteIndex(self, write_index: bool) → None: Returns whether to write an index at the end of the file (e.g. indexedmzML file format)

setWriteSupplementalData(self, in_0: bool) → None: Sets whether or not to write supplemental peak data in MzData files