MSChromatogram#

class pyopenms.MSChromatogram#

Bases: object

Cython implementation of _MSChromatogram

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1MSChromatogram.html

– Inherits from [‘ChromatogramSettings’, ‘RangeManagerRtInt’]

The representation of a chromatogram. Raw data access is proved by get_peaks and set_peaks, which yields numpy arrays Iterations yields access to underlying peak objects but is slower Extra data arrays can be accessed through getFloatDataArrays / getIntegerDataArrays / getStringDataArrays See help(ChromatogramSettings) for information about meta-information —– Usage:

precursor = chromatogram.getPrecursor() product = chromatogram.getProduct() rt, intensities = chromatogram.get_peaks()

__init__()#

Cython signature: void MSChromatogram()
Cython signature: void MSChromatogram(MSChromatogram &)

Methods

`__init__`	Cython signature: void MSChromatogram()
`clear`	Cython signature: void clear(int)
`clearMetaInfo`	Cython signature: void clearMetaInfo() Removes all meta values
`clearRanges`	Cython signature: void clearRanges() Resets all range dimensions as empty
`findNearest`	Cython signature: int findNearest(double)
`getAcquisitionInfo`	Cython signature: AcquisitionInfo getAcquisitionInfo() Returns the acquisition info
`getChromatogramType`	Cython signature: ChromatogramType getChromatogramType() Get the chromatogram type
`getComment`	Cython signature: String getComment() Returns the free-text comment
`getDataProcessing`	Cython signature: libcpp_vector[shared_ptr[DataProcessing]] getDataProcessing() Returns the description of the applied processing
`getFloatDataArrays`	Cython signature: libcpp_vector[FloatDataArray] getFloatDataArrays() Returns a reference to the float meta data arrays
`getInstrumentSettings`	Cython signature: InstrumentSettings getInstrumentSettings() Returns the instrument settings of the current spectrum
`getIntegerDataArrays`	Cython signature: libcpp_vector[IntegerDataArray] getIntegerDataArrays() Returns a reference to the integer meta data arrays
`getKeys`	Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
`getMZ`	Cython signature: double getMZ() Returns the mz of the product entry, makes sense especially for MRM scans
`getMaxIntensity`	Cython signature: double getMaxIntensity() Returns the maximum intensity
`getMaxRT`	Cython signature: double getMaxRT() Returns the maximum RT
`getMetaValue`	Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
`getMinIntensity`	Cython signature: double getMinIntensity() Returns the minimum intensity
`getMinRT`	Cython signature: double getMinRT() Returns the minimum RT
`getName`	Cython signature: String getName() Returns the name
`getNativeID`	Cython signature: String getNativeID() Returns the native identifier for the spectrum, used by the acquisition software.
`getPrecursor`	Cython signature: Precursor getPrecursor() Returns the precursors
`getProduct`	Cython signature: Product getProduct() Returns the product ion
`getSourceFile`	Cython signature: SourceFile getSourceFile() Returns the source file
`getStringDataArrays`	Cython signature: libcpp_vector[StringDataArray] getStringDataArrays() Returns a reference to the string meta data arrays
`get_peaks`
`isMetaEmpty`	Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
`isSorted`	Cython signature: bool isSorted() Checks if all peaks are sorted with respect to ascending RT
`metaRegistry`	Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
`metaValueExists`	Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
`push_back`	Cython signature: void push_back(ChromatogramPeak) Append a peak
`removeMetaValue`	Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
`reserve`	Cython signature: void reserve(size_t n)
`resize`	Cython signature: void resize(size_t n) Resize the peak array
`setAcquisitionInfo`	Cython signature: void setAcquisitionInfo(AcquisitionInfo acquisition_info) Sets the acquisition info
`setChromatogramType`	Cython signature: void setChromatogramType(ChromatogramType type) Sets the chromatogram type
`setComment`	Cython signature: void setComment(String comment) Sets the free-text comment
`setDataProcessing`	Cython signature: void setDataProcessing(libcpp_vector[shared_ptr[DataProcessing]]) Sets the description of the applied processing
`setFloatDataArrays`	Cython signature: void setFloatDataArrays(libcpp_vector[FloatDataArray] fda) Sets the float meta data arrays
`setInstrumentSettings`	Cython signature: void setInstrumentSettings(InstrumentSettings instrument_settings) Sets the instrument settings of the current spectrum
`setIntegerDataArrays`	Cython signature: void setIntegerDataArrays(libcpp_vector[IntegerDataArray] ida) Sets the integer meta data arrays
`setMetaValue`	Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
`setName`	Cython signature: void setName(String) Sets the name
`setNativeID`	Cython signature: void setNativeID(String native_id) Sets the native identifier for the spectrum, used by the acquisition software.
`setPrecursor`	Cython signature: void setPrecursor(Precursor precursor) Sets the precursors
`setProduct`	Cython signature: void setProduct(Product p) Sets the product ion
`setSourceFile`	Cython signature: void setSourceFile(SourceFile source_file) Sets the source file
`setStringDataArrays`	Cython signature: void setStringDataArrays(libcpp_vector[StringDataArray] sda) Sets the string meta data arrays
`set_peaks`
`size`	Cython signature: size_t size()
`sortByIntensity`	Cython signature: void sortByIntensity(bool reverse)
`sortByPosition`	Cython signature: void sortByPosition()
`updateRanges`	Cython signature: void updateRanges()

clear()#

Cython signature: void clear(int)

Parameters: clear_meta_data – If true, all meta data is cleared in addition to the data

clearMetaInfo()#: Cython signature: void clearMetaInfo() Removes all meta values

clearRanges()#: Cython signature: void clearRanges() Resets all range dimensions as empty

findNearest()#

Cython signature: int findNearest(double)

Parameters: rt – The searched for mass-to-charge ratio searched
Returns: Returns the index of the peak.

Note: Make sure the chromatogram is sorted with respect to RT! Otherwise the result is undefined

Raises: Exception: Precondition is thrown if the chromatogram is empty (not only in debug mode)

getAcquisitionInfo()#: Cython signature: AcquisitionInfo getAcquisitionInfo() Returns the acquisition info

getChromatogramType()#: Cython signature: ChromatogramType getChromatogramType() Get the chromatogram type

getComment()#: Cython signature: String getComment() Returns the free-text comment

getDataProcessing()#: Cython signature: libcpp_vector[shared_ptr[DataProcessing]] getDataProcessing() Returns the description of the applied processing

getFloatDataArrays()#: Cython signature: libcpp_vector[FloatDataArray] getFloatDataArrays() Returns a reference to the float meta data arrays

getInstrumentSettings()#: Cython signature: InstrumentSettings getInstrumentSettings() Returns the instrument settings of the current spectrum

getIntegerDataArrays()#: Cython signature: libcpp_vector[IntegerDataArray] getIntegerDataArrays() Returns a reference to the integer meta data arrays

getKeys()#: Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set

getMZ()#: Cython signature: double getMZ() Returns the mz of the product entry, makes sense especially for MRM scans

getMaxIntensity()#: Cython signature: double getMaxIntensity() Returns the maximum intensity

getMaxRT()#: Cython signature: double getMaxRT() Returns the maximum RT

getMetaValue()#: Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or

getMinIntensity()#: Cython signature: double getMinIntensity() Returns the minimum intensity

getMinRT()#: Cython signature: double getMinRT() Returns the minimum RT

getName()#: Cython signature: String getName() Returns the name

getNativeID()#: Cython signature: String getNativeID() Returns the native identifier for the spectrum, used by the acquisition software.

getPrecursor()#: Cython signature: Precursor getPrecursor() Returns the precursors

getProduct()#: Cython signature: Product getProduct() Returns the product ion

getSourceFile()#: Cython signature: SourceFile getSourceFile() Returns the source file

getStringDataArrays()#: Cython signature: libcpp_vector[StringDataArray] getStringDataArrays() Returns a reference to the string meta data arrays

get_peaks()#

isMetaEmpty()#: Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty

isSorted()#: Cython signature: bool isSorted() Checks if all peaks are sorted with respect to ascending RT

metaRegistry()#: Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry

metaValueExists()#: Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists

push_back()#: Cython signature: void push_back(ChromatogramPeak) Append a peak

removeMetaValue()#: Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists

reserve()#: Cython signature: void reserve(size_t n)

resize()#: Cython signature: void resize(size_t n) Resize the peak array

setAcquisitionInfo()#: Cython signature: void setAcquisitionInfo(AcquisitionInfo acquisition_info) Sets the acquisition info

setChromatogramType()#: Cython signature: void setChromatogramType(ChromatogramType type) Sets the chromatogram type

setComment()#: Cython signature: void setComment(String comment) Sets the free-text comment

setDataProcessing()#: Cython signature: void setDataProcessing(libcpp_vector[shared_ptr[DataProcessing]]) Sets the description of the applied processing

setFloatDataArrays()#: Cython signature: void setFloatDataArrays(libcpp_vector[FloatDataArray] fda) Sets the float meta data arrays

setInstrumentSettings()#: Cython signature: void setInstrumentSettings(InstrumentSettings instrument_settings) Sets the instrument settings of the current spectrum

setIntegerDataArrays()#: Cython signature: void setIntegerDataArrays(libcpp_vector[IntegerDataArray] ida) Sets the integer meta data arrays

setMetaValue()#: Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name

setName()#: Cython signature: void setName(String) Sets the name

setNativeID()#: Cython signature: void setNativeID(String native_id) Sets the native identifier for the spectrum, used by the acquisition software.

setPrecursor()#: Cython signature: void setPrecursor(Precursor precursor) Sets the precursors

setProduct()#: Cython signature: void setProduct(Product p) Sets the product ion

setSourceFile()#: Cython signature: void setSourceFile(SourceFile source_file) Sets the source file

setStringDataArrays()#: Cython signature: void setStringDataArrays(libcpp_vector[StringDataArray] sda) Sets the string meta data arrays

set_peaks()#

size()#: Cython signature: size_t size()

sortByIntensity()#

Cython signature: void sortByIntensity(bool reverse)

Sorts the peaks according to ascending intensity. Meta data arrays will be sorted accordingly

sortByPosition()#

Cython signature: void sortByPosition()

The chromatogram is sorted with respect to position. Meta data arrays will be sorted accordingly

updateRanges()#: Cython signature: void updateRanges()