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
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
Sets numpress configuration options for float data arrays
Sets numpress configuration options for intensity dimension
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
- getMSLevels(self) List[int] #
Returns the set MS levels
- 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
- 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
- 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
- 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