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