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()