PeakFileOptions#

class pyopenms.PeakFileOptions#

Bases: object

Cython implementation of _PeakFileOptions

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1PeakFileOptions.html

Options for loading files containing peak data

__init__()#

Cython signature: void PeakFileOptions()
Cython signature: void PeakFileOptions(PeakFileOptions &)

Methods

`__init__`	Cython signature: void PeakFileOptions()
`addMSLevel`	Cython signature: void addMSLevel(int level) Adds a desired MS level for peaks to load
`clearMSLevels`	Cython signature: void clearMSLevels() Clears the MS levels
`containsMSLevel`	Cython signature: bool containsMSLevel(int level) Returns true, if MS level level has been set
`getCompression`	Cython signature: bool getCompression() Returns true, if data should be compressed when writing
`getFillData`	Cython signature: bool getFillData() Returns whether to fill the actual data into the container (spectrum/chromatogram)
`getForceMQCompatability`	Cython signature: bool getForceMQCompatability() [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`	Cython signature: bool getForceTPPCompatability() [mzML only!]Returns Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z
`getIntensity32Bit`	Cython signature: bool getIntensity32Bit() Returns true, if intensity data should be stored with 32bit precision
`getIntensityRange`	Cython signature: DRange1 getIntensityRange() Returns the intensity range
`getMSLevels`	Cython signature: libcpp_vector[int] getMSLevels() Returns the set MS levels
`getMZRange`	Cython signature: DRange1 getMZRange() Returns the MZ range
`getMaxDataPoolSize`	Cython signature: size_t getMaxDataPoolSize() Returns maximal size of the data pool
`getMetadataOnly`	Cython signature: bool getMetadataOnly() Returns whether or not to load only meta data
`getMz32Bit`	Cython signature: bool getMz32Bit() Returns true, if mz-data and rt-data should be stored with 32bit precision
`getNumpressConfigurationFloatDataArray`	Cython signature: NumpressConfig getNumpressConfigurationFloatDataArray() Sets numpress configuration options for float data arrays
`getNumpressConfigurationIntensity`	Cython signature: NumpressConfig getNumpressConfigurationIntensity() Sets numpress configuration options for intensity dimension
`getNumpressConfigurationMassTime`	Cython signature: NumpressConfig getNumpressConfigurationMassTime() Sets numpress configuration options for m/z or rt dimension
`getRTRange`	Cython signature: DRange1 getRTRange() Returns the RT range
`getSkipXMLChecks`	Cython signature: bool getSkipXMLChecks() Returns whether to skip some XML checks and be fast instead
`getSortChromatogramsByRT`	Cython signature: bool getSortChromatogramsByRT() Returns whether or not peaks in chromatograms should be sorted
`getSortSpectraByMZ`	Cython signature: bool getSortSpectraByMZ() Returns whether or not peaks in spectra should be sorted
`getWriteIndex`	Cython signature: bool getWriteIndex() Returns whether to write an index at the end of the file (e.g.
`getWriteSupplementalData`	Cython signature: bool getWriteSupplementalData() Returns whether or not to write supplemental peak data in MzData files
`hasFilters`	Cython signature: bool hasFilters()
`hasIntensityRange`	Cython signature: bool hasIntensityRange() Returns true if an intensity range has been set
`hasMSLevels`	Cython signature: bool hasMSLevels() Returns true, if MS levels have been set
`hasMZRange`	Cython signature: bool hasMZRange() Returns true if an MZ range has been set
`hasRTRange`	Cython signature: bool hasRTRange() Returns true if an RT range has been set
`setCompression`	Cython signature: void setCompression(bool) Sets if data should be compressed when writing
`setFillData`	Cython signature: void setFillData(bool only) Sets whether to fill the actual data into the container (spectrum/chromatogram)
`setForceMQCompatability`	Cython signature: void setForceMQCompatability(bool 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`	Cython signature: void setForceTPPCompatability(bool forceTPP) [ mzML only!]Returns Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z
`setIntensity32Bit`	Cython signature: void setIntensity32Bit(bool int_32_bit) Sets if intensity data should be stored with 32bit or 64bit precision
`setIntensityRange`	Cython signature: void setIntensityRange(DRange1 & range_) Restricts the range of intensity values for peaks to load
`setMSLevels`	Cython signature: void setMSLevels(libcpp_vector[int] levels) Sets the desired MS levels for peaks to load
`setMZRange`	Cython signature: void setMZRange(DRange1 & range_) Restricts the range of MZ values for peaks to load
`setMaxDataPoolSize`	Cython signature: void setMaxDataPoolSize(size_t s) Sets maximal size of the data pool
`setMetadataOnly`	Cython signature: void setMetadataOnly(bool) Sets whether or not to load only meta data
`setMz32Bit`	Cython signature: void setMz32Bit(bool mz_32_bit) Sets if mz-data and rt-data should be stored with 32bit or 64bit precision
`setNumpressConfigurationFloatDataArray`	Cython signature: void setNumpressConfigurationFloatDataArray(NumpressConfig config) Returns numpress configuration options for float data arrays
`setNumpressConfigurationIntensity`	Cython signature: void setNumpressConfigurationIntensity(NumpressConfig config) Returns numpress configuration options for intensity dimension
`setNumpressConfigurationMassTime`	Cython signature: void setNumpressConfigurationMassTime(NumpressConfig config) Returns numpress configuration options for m/z or rt dimension
`setRTRange`	Cython signature: void setRTRange(DRange1 & range_) Restricts the range of RT values for peaks to load
`setSkipXMLChecks`	Cython signature: void setSkipXMLChecks(bool only) Sets whether to skip some XML checks and be fast instead
`setSortChromatogramsByRT`	Cython signature: void setSortChromatogramsByRT(bool doSort) Sets whether or not to sort peaks in chromatograms
`setSortSpectraByMZ`	Cython signature: void setSortSpectraByMZ(bool doSort) Sets whether or not to sort peaks in spectra
`setWriteIndex`	Cython signature: void setWriteIndex(bool write_index) Returns whether to write an index at the end of the file (e.g.
`setWriteSupplementalData`	Cython signature: void setWriteSupplementalData(bool) Sets whether or not to write supplemental peak data in MzData files

addMSLevel()#: Cython signature: void addMSLevel(int level) Adds a desired MS level for peaks to load

clearMSLevels()#: Cython signature: void clearMSLevels() Clears the MS levels

containsMSLevel()#: Cython signature: bool containsMSLevel(int level) Returns true, if MS level level has been set

getCompression()#: Cython signature: bool getCompression() Returns true, if data should be compressed when writing

getFillData()#: Cython signature: bool getFillData() Returns whether to fill the actual data into the container (spectrum/chromatogram)

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

getIntensity32Bit()#: Cython signature: bool getIntensity32Bit() Returns true, if intensity data should be stored with 32bit precision

getIntensityRange()#: Cython signature: DRange1 getIntensityRange() Returns the intensity range

getMSLevels()#: Cython signature: libcpp_vector[int] getMSLevels() Returns the set MS levels

getMZRange()#: Cython signature: DRange1 getMZRange() Returns the MZ range

getMaxDataPoolSize()#: Cython signature: size_t getMaxDataPoolSize() Returns maximal size of the data pool

getMetadataOnly()#: Cython signature: bool getMetadataOnly() Returns whether or not to load only meta data

getMz32Bit()#: Cython signature: bool getMz32Bit() Returns true, if mz-data and rt-data should be stored with 32bit precision

getNumpressConfigurationFloatDataArray()#: Cython signature: NumpressConfig getNumpressConfigurationFloatDataArray() Sets numpress configuration options for float data arrays

getNumpressConfigurationIntensity()#: Cython signature: NumpressConfig getNumpressConfigurationIntensity() Sets numpress configuration options for intensity dimension

getNumpressConfigurationMassTime()#: Cython signature: NumpressConfig getNumpressConfigurationMassTime() Sets numpress configuration options for m/z or rt dimension

getRTRange()#: Cython signature: DRange1 getRTRange() Returns the RT range

getSkipXMLChecks()#: Cython signature: bool getSkipXMLChecks() Returns whether to skip some XML checks and be fast instead

getSortChromatogramsByRT()#: Cython signature: bool getSortChromatogramsByRT() Returns whether or not peaks in chromatograms should be sorted

getSortSpectraByMZ()#: Cython signature: bool getSortSpectraByMZ() Returns whether or not peaks in spectra should be sorted

getWriteIndex()#: Cython signature: bool getWriteIndex() Returns whether to write an index at the end of the file (e.g. indexedmzML file format)

getWriteSupplementalData()#: Cython signature: bool getWriteSupplementalData() Returns whether or not to write supplemental peak data in MzData files

hasFilters()#: Cython signature: bool hasFilters()

hasIntensityRange()#: Cython signature: bool hasIntensityRange() Returns true if an intensity range has been set

hasMSLevels()#: Cython signature: bool hasMSLevels() Returns true, if MS levels have been set

hasMZRange()#: Cython signature: bool hasMZRange() Returns true if an MZ range has been set

hasRTRange()#: Cython signature: bool hasRTRange() Returns true if an RT range has been set

setCompression()#: Cython signature: void setCompression(bool) Sets if data should be compressed when writing

setFillData()#: Cython signature: void setFillData(bool only) Sets whether to fill the actual data into the container (spectrum/chromatogram)

setForceMQCompatability()#: Cython signature: void setForceMQCompatability(bool 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()#: Cython signature: void setForceTPPCompatability(bool forceTPP) [ mzML only!]Returns Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z

setIntensity32Bit()#: Cython signature: void setIntensity32Bit(bool int_32_bit) Sets if intensity data should be stored with 32bit or 64bit precision

setIntensityRange()#: Cython signature: void setIntensityRange(DRange1 & range_) Restricts the range of intensity values for peaks to load

setMSLevels()#: Cython signature: void setMSLevels(libcpp_vector[int] levels) Sets the desired MS levels for peaks to load

setMZRange()#: Cython signature: void setMZRange(DRange1 & range_) Restricts the range of MZ values for peaks to load

setMaxDataPoolSize()#: Cython signature: void setMaxDataPoolSize(size_t s) Sets maximal size of the data pool

setMetadataOnly()#: Cython signature: void setMetadataOnly(bool) Sets whether or not to load only meta data

setMz32Bit()#: Cython signature: void setMz32Bit(bool mz_32_bit) Sets if mz-data and rt-data should be stored with 32bit or 64bit precision

setNumpressConfigurationFloatDataArray()#: Cython signature: void setNumpressConfigurationFloatDataArray(NumpressConfig config) Returns numpress configuration options for float data arrays

setNumpressConfigurationIntensity()#: Cython signature: void setNumpressConfigurationIntensity(NumpressConfig config) Returns numpress configuration options for intensity dimension

setNumpressConfigurationMassTime()#: Cython signature: void setNumpressConfigurationMassTime(NumpressConfig config) Returns numpress configuration options for m/z or rt dimension

setRTRange()#: Cython signature: void setRTRange(DRange1 & range_) Restricts the range of RT values for peaks to load

setSkipXMLChecks()#: Cython signature: void setSkipXMLChecks(bool only) Sets whether to skip some XML checks and be fast instead

setSortChromatogramsByRT()#: Cython signature: void setSortChromatogramsByRT(bool doSort) Sets whether or not to sort peaks in chromatograms

setSortSpectraByMZ()#: Cython signature: void setSortSpectraByMZ(bool doSort) Sets whether or not to sort peaks in spectra

setWriteIndex()#: Cython signature: void setWriteIndex(bool write_index) Returns whether to write an index at the end of the file (e.g. indexedmzML file format)

setWriteSupplementalData()#: Cython signature: void setWriteSupplementalData(bool) Sets whether or not to write supplemental peak data in MzData files